From witzjean at gmail.com  Sat Dec  1 05:34:10 2012
From: witzjean at gmail.com (jeff witz)
Date: Sat, 1 Dec 2012 02:34:10 -0800 (PST)
Subject: Making algorithms at least 3D, preferably nD
In-Reply-To: <CA+JHcKTOLe0P-014dNc90C+6xP+LrcA+Pz3y5BkJQx59AqLw5g@mail.gmail.com>
References: <CA+JHcKTOLe0P-014dNc90C+6xP+LrcA+Pz3y5BkJQx59AqLw5g@mail.gmail.com>
Message-ID: <ec2a5e61-8545-410e-93cf-a4862ec4edc7@googlegroups.com>

Hello,

I think you must all pay attention to standards if you want to act on nD 
images. For structured data files there is a library that hab been used for 
decade and which is very efficient, it's netcdf 
(http://www.unidata.ucar.edu/software/netcdf/), there is already tools in 
python to deal with it. This library allows one to deal with data in // 
which is important when one deals with big datas. The last version is based 
on hdf wich is the tools used on HPC.

If your data are not stored in a standard format, the library ITK has 
provide a binding called SimpleITK that allows one to read every format ITK 
konws. 

It is important to take into account the fact that the operation on pixel 
depend on the grid spacing, as for exampe the finite difference gradient 
which is wrong when one chooses a step of one because the file as not been 
read correctly.

As the 3D datas often comes from the measurement X-Ray Tomography, MRI, 
Echography, it is important to consider the device information. The format 
dicom as been made in this specific purpose there is a python binding 
called pydicom. 

I know that scikit team does'nt want to have to much dependances, but for 
nD case I think it is important to use existing libraries.

Best regards




Le vendredi 30 novembre 2012 05:45:49 UTC+1, Juan Nunez-Iglesias a ?crit :
>
> Hey Guys,
>
> I mentioned this briefly at SciPy, but I would like to reiterate: a lot of 
> data is 3D images these days, and more and more data is being generated 
> that is multi-channel, 3D+t. Therefore, it would be awesome if scikit-image 
> started making more of an effort to support these. In the best case, the 
> dimension of the underlying array can be abstracted away ? see here<https://github.com/jni/ray/blob/develop/ray/morpho.py#L328>for example, the functions juicy_center (which extracts the centre of an 
> array, along all dimensions), surfaces (grabs the "border" arrays along 
> each dimension), hollowed (zeroes-out the centre), and more. Otherwise, 
> writing a 3D function that gracefully degrades to 2D when one of the 
> dimensions is 1 is also possible.
>
> In general, the amount of additional effort to make code 3-, 4- or n- 
> dimensional is relatively low when you write the algorithm initially, 
> relative to refactoring a whole bunch of functions later. I'll try to 
> fiddle with whichever code I need, but in the meantime, what do you think 
> about adding a paragraph or a sentence about this issue in the scikit-image 
> contribute <http://scikit-image.org/docs/dev/contribute.html> section, so 
> that people at least have this in mind when they are thinking of writing 
> something new?
>
> Thanks,
>
> Juan.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121201/703463a5/attachment.html>

From stefan at sun.ac.za  Thu Dec  6 16:06:07 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 6 Dec 2012 13:06:07 -0800
Subject: Hello, everyone
In-Reply-To: <de6330ad-506e-4d1a-8982-8bf1f1ab6c2b@googlegroups.com>
References: <de6330ad-506e-4d1a-8982-8bf1f1ab6c2b@googlegroups.com>
Message-ID: <CABDkGQkqWGNKrXGstvYXWdrONk8iohP5=UhxfrYKyF2YfQpy3w@mail.gmail.com>

Hi there,

On Wed, Dec 5, 2012 at 5:58 PM, Han Cao <simonda72819 at gmail.com> wrote:
> I am new guy to this group. I am a student who want to get some development
> experiences to image processing products. So I choose scikit-image. I want
> to contribute to this product.
> I hope to know is there any products using this library now? Thanks a lot if
> anyone answer me?

Welcome, I hope you find the project useful!

Are you asking about commercial products specifically, or research
projects in general?  Scikit-image has found all sorts of interesting
applications, ranging from astronomy to biology to computer vision.  I
think it would be a good idea to gather more such "user stories"!

St?fan


From simonda72819 at gmail.com  Fri Dec  7 03:18:39 2012
From: simonda72819 at gmail.com (caohan)
Date: Fri, 07 Dec 2012 16:18:39 +0800
Subject: Hello, everyone
In-Reply-To: <CABDkGQkqWGNKrXGstvYXWdrONk8iohP5=UhxfrYKyF2YfQpy3w@mail.gmail.com>
References: <de6330ad-506e-4d1a-8982-8bf1f1ab6c2b@googlegroups.com> <CABDkGQkqWGNKrXGstvYXWdrONk8iohP5=UhxfrYKyF2YfQpy3w@mail.gmail.com>
Message-ID: <50C1A65F.7050509@gmail.com>

On 12/07/2012 05:06 AM, St??????fan van der Walt wrote:
> Hi there,
>
> On Wed, Dec 5, 2012 at 5:58 PM, Han Cao <simonda72819 at gmail.com> wrote:
>> I am new guy to this group. I am a student who want to get some development
>> experiences to image processing products. So I choose scikit-image. I want
>> to contribute to this product.
>> I hope to know is there any products using this library now? Thanks a lot if
>> anyone answer me?
> Welcome, I hope you find the project useful!
>
> Are you asking about commercial products specifically, or research
> projects in general?  Scikit-image has found all sorts of interesting
> applications, ranging from astronomy to biology to computer vision.  I
> think it would be a good idea to gather more such "user stories"!
>
> St??????fan
>
Thank you for replying me, I am asking about commercial products, such 
as Matlab?

Hank Cao


From steven.silvester at gmail.com  Thu Dec 13 22:42:04 2012
From: steven.silvester at gmail.com (Steven Silvester)
Date: Thu, 13 Dec 2012 19:42:04 -0800 (PST)
Subject: import speedup
Message-ID: <72c15392-9d66-4153-9f26-8c7b2b06c6c4@googlegroups.com>

Hey all, I noticed that loading skimage seemed to take a bit longer than 
I'd like, so I profiled it.  On my machine, it takes 1.6 seconds to import 
skimage, 0.4 of which was from numpy, and 1.2 of which was from loading 
nose in skimage/__init__.py.  This simple patch brings my import time down 
to ~0.4 seconds, since it only imports nose when the test function is 
called.

diff --git a/skimage/__init__.py b/skimage/__init__.py
index 1ac121b..f3e5e88 100644
--- a/skimage/__init__.py
+++ b/skimage/__init__.py
@@ -84,8 +84,9 @@ def _setup_test(verbose=False):
         return f
 
 
-test = _setup_test()
-test_verbose = _setup_test(verbose=True)
+test = lambda : _setup_test()()
+test_verbose = lambda : _setup_test(verbose=True)()
+test_verbose.__doc__ = test.__doc__ = 'Invoke the skimage test suite.'
 
 
 def get_log(name=None):

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121213/0bb18033/attachment.html>

From silvertrumpet999 at gmail.com  Thu Dec 13 23:22:00 2012
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 13 Dec 2012 20:22:00 -0800 (PST)
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com>
Message-ID: <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com>

Hi Parand,

Welcome!  Most of the gallery examples work in the current release (0.7.2 I 
believe), but the rank filter is in a PR that was merged recently, and is 
presently only in the dev version.  You may want the functionality in the 
rank filter for OCR work, where fast local operations like the otsu 
threshold could be very beneficial.  

I'll let other people answer the questions about specific references as I'm 
on the road, but I think most of what you need to do is available in 
scikit-image.

Josh Warner


On Wednesday, December 12, 2012 7:00:24 PM UTC-6, Parand Darugar wrote:
>
> Hello,
>
> I'm new to scikit-image, having mostly used PIL and imagemagick to date. 
> Looks very promising, thanks for putting it together.
>
> A few newbie questions:
>
> - It seems the examples in the gallery are based on the dev version as 
> opposed to the stable version? Therefore I assume it's recommended to use 
> the dev version instead of the "pip install" version? I just tried the 
> latest from git and am getting some errors (see below) - which version 
> should I be using?
>
> - My initial goal is image/document enhancement and cleanup in order to 
> improve OCR. The images are primarily captured via cell phone cameras and 
> scanners, so I'm looking to normalize and enhance the color, remove noise, 
> and straighten them. Any pointers to code, papers, or algorithms that may 
> be of interest would be appreciated.
>
> -- Error message --
> >>> import skimage.filter.rank as rank
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "skimage/filter/__init__.py", line 2, in <module>
>     from .ctmf import median_filter
>   File "skimage/filter/ctmf.py", line 15, in <module>
>     from . import _ctmf
> ImportError: cannot import name _ctmf
>
> Much thanks,
>
> Parand
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121213/8c8a61ef/attachment.html>

From silvertrumpet999 at gmail.com  Thu Dec 13 23:25:49 2012
From: silvertrumpet999 at gmail.com (Josh Warner)
Date: Thu, 13 Dec 2012 20:25:49 -0800 (PST)
Subject: import speedup
In-Reply-To: <72c15392-9d66-4153-9f26-8c7b2b06c6c4@googlegroups.com>
References: <72c15392-9d66-4153-9f26-8c7b2b06c6c4@googlegroups.com>
Message-ID: <14a17e6a-3d3f-4865-81e5-d1c2e8b845b9@googlegroups.com>

I say toss it in a PR, and assuming the Travis build passes this sounds 
completely reasonable to me.  

On Thursday, December 13, 2012 9:42:04 PM UTC-6, Steven Silvester wrote:
>
> Hey all, I noticed that loading skimage seemed to take a bit longer than 
> I'd like, so I profiled it.  On my machine, it takes 1.6 seconds to import 
> skimage, 0.4 of which was from numpy, and 1.2 of which was from loading 
> nose in skimage/__init__.py.  This simple patch brings my import time down 
> to ~0.4 seconds, since it only imports nose when the test function is 
> called.
>
> diff --git a/skimage/__init__.py b/skimage/__init__.py
> index 1ac121b..f3e5e88 100644
> --- a/skimage/__init__.py
> +++ b/skimage/__init__.py
> @@ -84,8 +84,9 @@ def _setup_test(verbose=False):
>          return f
>  
>  
> -test = _setup_test()
> -test_verbose = _setup_test(verbose=True)
> +test = lambda : _setup_test()()
> +test_verbose = lambda : _setup_test(verbose=True)()
> +test_verbose.__doc__ = test.__doc__ = 'Invoke the skimage test suite.'
>  
>  
>  def get_log(name=None):
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121213/645a2fcf/attachment.html>

From stefan at sun.ac.za  Fri Dec 14 00:28:11 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 13 Dec 2012 21:28:11 -0800
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com>
 <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com> <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>
Message-ID: <CABDkGQ=Pd0T2qLdiLoPVv2JaLcAVrxWSVLW1umQB5GK+VUbe7Q@mail.gmail.com>

On Thu, Dec 13, 2012 at 8:54 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> It might be a good idea for us to point to the stable version instead of the
> development version by default.

The development gallery is useful as an advertisement, but we could
maybe make the link to the other versions clearer?

St?fan


From tsyu80 at gmail.com  Thu Dec 13 22:43:13 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 13 Dec 2012 22:43:13 -0500
Subject: canvastools subpackage for scikit-image viewer
Message-ID: <CAEym_HqXtdb91_YJtNG4-CWS1XWk9azaa=G34WXZuMH7C+Kbrw@mail.gmail.com>

About a month-or-so ago, I promised I would start work on selection tool
for the image viewer. I finally got around to it. I ended up doing a pretty
significant overhaul, but I think it was worth it.

See PR # 390 <https://github.com/scikit-image/scikit-image/pull/390>

I'll copy my PR message below, just for completeness:


Major overhaul of tools for interacting with the scikit-image viewer.

* Add skimage.viewer.canvastools subpackage with line and rectangle
selection tools
* Refactor line profile plugin to use line tool
* Fix viewer canvas
* Fix blitting behavior
* New plugins (ColorHistogram, Measure, Crop)

To get a feel for the changes, see new examples in
`viewer_examples/plugins` located in the root directory of package.

Cheers,
-Tony
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121213/d94c2c83/attachment.html>

From tsyu80 at gmail.com  Thu Dec 13 23:54:00 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Thu, 13 Dec 2012 23:54:00 -0500
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com> <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com>
Message-ID: <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>

On Thu, Dec 13, 2012 at 11:22 PM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> Hi Parand,
>
> Welcome!  Most of the gallery examples work in the current release (0.7.2
> I believe), but the rank filter is in a PR that was merged recently, and is
> presently only in the dev version.  You may want the functionality in the
> rank filter for OCR work, where fast local operations like the otsu
> threshold could be very beneficial.
>
> I'll let other people answer the questions about specific references as
> I'm on the road, but I think most of what you need to do is available in
> scikit-image.
>
> Josh Warner
>

Just wanted to add: The documentation for the last release can be found
here:

http://scikit-image.org/docs/0.7.0/


It might be a good idea for us to point to the stable version instead of
the development version by default.



On Wednesday, December 12, 2012 7:00:24 PM UTC-6, Parand Darugar wrote:
>>
>>
>> <snip>

> - My initial goal is image/document enhancement and cleanup in order to
>> improve OCR. The images are primarily captured via cell phone cameras and
>> scanners, so I'm looking to normalize and enhance the color, remove noise,
>> and straighten them. Any pointers to code, papers, or algorithms that may
>> be of interest would be appreciated.
>>
>> -- Error message --
>> >>> import skimage.filter.rank as rank
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File "skimage/filter/__init__.py", line 2, in <module>
>>     from .ctmf import median_filter
>>   File "skimage/filter/ctmf.py", line 15, in <module>
>>     from . import _ctmf
>> ImportError: cannot import name _ctmf
>>
>
This shouldn't happen. How did you install scikit-image? Are you sure that
you built the package after downloading.

Cheers,
-Tony
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121213/c6d3a506/attachment.html>

From steven.silvester at gmail.com  Fri Dec 14 11:14:18 2012
From: steven.silvester at gmail.com (Steven Silvester)
Date: Fri, 14 Dec 2012 08:14:18 -0800 (PST)
Subject: canvastools subpackage for scikit-image viewer
In-Reply-To: <CAEym_HqXtdb91_YJtNG4-CWS1XWk9azaa=G34WXZuMH7C+Kbrw@mail.gmail.com>
References: <CAEym_HqXtdb91_YJtNG4-CWS1XWk9azaa=G34WXZuMH7C+Kbrw@mail.gmail.com>
Message-ID: <3d65b13b-c793-4337-a1fa-764e4210b264@googlegroups.com>

Tony,

I'm going all in on this with you.  I have been hacking at matplotlib recently as well, and have demonstrated the following in PySide and PyQt4:
- right click menu with grid toggle and colormap selection, and simplified uimenu creation
- roi with stats overlay (mean, std, min, max)
- cross section slice view
- scroll zoom
- improved colorbar placement

I also wrote a tool in enaml that allows you to pick a skimage package and function from dropdowns. It then displays the docstring and allows you to write the function call inline, and safely evaluates it. 

Thus far, it has all been proof of concept and for use at work, but I'd like to start integrating these features into your viewer. 

I will start a repo on my github to demonstrate the features prior to integration. 

Thoughts?

From darugar at gmail.com  Fri Dec 14 13:31:27 2012
From: darugar at gmail.com (Parand Darugar)
Date: Fri, 14 Dec 2012 10:31:27 -0800 (PST)
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com> <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com>
 <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>
Message-ID: <66cc4b6d-2942-416a-a37a-d8fa196ce5df@googlegroups.com>

Hi Tony,

Installation steps:

This is on OS X 10.8.2, Python 2.7.2:

- I setup a virtualenv and activated that virtual env.
- I cloned the scikit-image git repository
- I installed:

$ python ./setup.py install
...
Installed 
/Users/parand/Projects/Receipts/pyenv/lib/python2.7/site-packages/scikit_image-0.8dev-py2.7-macosx-10.8-intel.egg
Processing dependencies for scikit-image==0.8dev
Finished processing dependencies for scikit-image==0.8dev

$ python
Python 2.7.2 (default, Jun 20 2012, 16:23:33) 
[GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin
>>> import skimage
>>> skimage.__version__
'0.8dev'
>>> import skimage.filter.rank as rank
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "skimage/filter/__init__.py", line 2, in <module>
    from .ctmf import median_filter
  File "skimage/filter/ctmf.py", line 15, in <module>
    from . import _ctmf
ImportError: cannot import name _ctmf

Best,

Parand

On Thursday, December 13, 2012 8:54:00 PM UTC-8, Tony S Yu wrote:
>
> On Thu, Dec 13, 2012 at 11:22 PM, Josh Warner <silvertr... at gmail.com<javascript:>
> > wrote:
>
>> Hi Parand,
>>
>> Welcome!  Most of the gallery examples work in the current release (0.7.2 
>> I believe), but the rank filter is in a PR that was merged recently, and is 
>> presently only in the dev version.  You may want the functionality in the 
>> rank filter for OCR work, where fast local operations like the otsu 
>> threshold could be very beneficial.  
>>
>> I'll let other people answer the questions about specific references as 
>> I'm on the road, but I think most of what you need to do is available in 
>> scikit-image.
>>
>> Josh Warner
>>
>
> Just wanted to add: The documentation for the last release can be found 
> here:
>
> http://scikit-image.org/docs/0.7.0/
>
>
> It might be a good idea for us to point to the stable version instead of 
> the development version by default.
>
>  
>
> On Wednesday, December 12, 2012 7:00:24 PM UTC-6, Parand Darugar wrote:
>>>
>>>
>>> <snip> 
>
>> - My initial goal is image/document enhancement and cleanup in order to 
>>> improve OCR. The images are primarily captured via cell phone cameras and 
>>> scanners, so I'm looking to normalize and enhance the color, remove noise, 
>>> and straighten them. Any pointers to code, papers, or algorithms that may 
>>> be of interest would be appreciated.
>>>
>>> -- Error message --
>>> >>> import skimage.filter.rank as rank
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File "skimage/filter/__init__.py", line 2, in <module>
>>>     from .ctmf import median_filter
>>>   File "skimage/filter/ctmf.py", line 15, in <module>
>>>     from . import _ctmf
>>> ImportError: cannot import name _ctmf
>>>
>>
> This shouldn't happen. How did you install scikit-image? Are you sure that 
> you built the package after downloading.
>  
> Cheers,
> -Tony
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121214/ff2b99f6/attachment.html>

From steven.silvester at gmail.com  Fri Dec 14 14:11:39 2012
From: steven.silvester at gmail.com (Steven Silvester)
Date: Fri, 14 Dec 2012 11:11:39 -0800 (PST)
Subject: canvastools subpackage for scikit-image viewer
In-Reply-To: <CAEym_Hr0e+sQ42r2ykXegXsChuUEYtU8rpEHdsanH0JTw4USog@mail.gmail.com>
References: <CAEym_HqXtdb91_YJtNG4-CWS1XWk9azaa=G34WXZuMH7C+Kbrw@mail.gmail.com>
 <3d65b13b-c793-4337-a1fa-764e4210b264@googlegroups.com>
 <CAEym_Hr0e+sQ42r2ykXegXsChuUEYtU8rpEHdsanH0JTw4USog@mail.gmail.com>
Message-ID: <fbc88d95-3178-48fc-8828-69443b219750@googlegroups.com>

Great, I'll dig into your PR this weekend.  I was thinking that each plugin could be registered as a dock window, and be switchable via a View menu. 

From tsyu80 at gmail.com  Fri Dec 14 11:37:17 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Fri, 14 Dec 2012 11:37:17 -0500
Subject: canvastools subpackage for scikit-image viewer
In-Reply-To: <3d65b13b-c793-4337-a1fa-764e4210b264@googlegroups.com>
References: <CAEym_HqXtdb91_YJtNG4-CWS1XWk9azaa=G34WXZuMH7C+Kbrw@mail.gmail.com>
 <3d65b13b-c793-4337-a1fa-764e4210b264@googlegroups.com>
Message-ID: <CAEym_Hr0e+sQ42r2ykXegXsChuUEYtU8rpEHdsanH0JTw4USog@mail.gmail.com>

On Fri, Dec 14, 2012 at 11:14 AM, Steven Silvester <
steven.silvester at gmail.com> wrote:

> Tony,
>
> I'm going all in on this with you.  I have been hacking at matplotlib
> recently as well, and have demonstrated the following in PySide and PyQt4:
> - right click menu with grid toggle and colormap selection, and simplified
> uimenu creation
> - roi with stats overlay (mean, std, min, max)
> - cross section slice view
> - scroll zoom
> - improved colorbar placement
>
> I also wrote a tool in enaml that allows you to pick a skimage package and
> function from dropdowns. It then displays the docstring and allows you to
> write the function call inline, and safely evaluates it.
>
> Thus far, it has all been proof of concept and for use at work, but I'd
> like to start integrating these features into your viewer.
>
> I will start a repo on my github to demonstrate the features prior to
> integration.
>
> Thoughts?
>
> --
>

Hey Steven,

That sounds fantastic!

I've tried to make a pretty solid API for the viewer, but since I'm the
only one playing with this code (as far as I know), it's tough to know
whether any of the infrastructure makes sense. It'd be great to have
someone else around to kick the tires and tell me what I did wrong.

As far as your suggestions, they all sound great. The "cross section slice
view", however, sounds similar to the lineprofile
plugin<https://github.com/scikit-image/scikit-image/blob/master/viewer_examples/plugins/lineprofile.py>that
Guillaume Gay wrote, so you may want to check that out first. I've
been wanting to add some sort of menu interface to access the plugins, so
it'd be great if you already have something. Also, I think the ROI stats
viewer would be a pretty good example of the RectangleTool added in this PR.

I'm looking forward to seeing some more PRs from you :)

Best,
-Tony
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121214/e92a0730/attachment.html>

From hannesschoenberger at gmail.com  Fri Dec 14 08:26:12 2012
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Sch=F6nberger_Johannes?=)
Date: Fri, 14 Dec 2012 14:26:12 +0100
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <CABDkGQ=Pd0T2qLdiLoPVv2JaLcAVrxWSVLW1umQB5GK+VUbe7Q@mail.gmail.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com> <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com> <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com> <CABDkGQ=Pd0T2qLdiLoPVv2JaLcAVrxWSVLW1umQB5GK+VUbe7Q@mail.gmail.com>
Message-ID: <02582B6B-4C51-4153-894D-7E7B64DAB5ED@gmail.com>

Maybe the "Gallery" link in the navigation should point to the dev gallery and the "Documentation" link to the stable docs?


From tsyu80 at gmail.com  Fri Dec 14 14:37:32 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Fri, 14 Dec 2012 14:37:32 -0500
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <66cc4b6d-2942-416a-a37a-d8fa196ce5df@googlegroups.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com>
 <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com> <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>
 <66cc4b6d-2942-416a-a37a-d8fa196ce5df@googlegroups.com>
Message-ID: <CAEym_Hom=Qzx94a+sB7NyTmx5f1i7m1RZB=+1rPfYVkj87gb9A@mail.gmail.com>

On Fri, Dec 14, 2012 at 1:31 PM, Parand Darugar <darugar at gmail.com> wrote:

> Hi Tony,
>
> Installation steps:
>
> This is on OS X 10.8.2, Python 2.7.2:
>
> - I setup a virtualenv and activated that virtual env.
> - I cloned the scikit-image git repository
> - I installed:
>
> $ python ./setup.py install
> ...
> Installed
> /Users/parand/Projects/Receipts/pyenv/lib/python2.7/site-packages/scikit_image-0.8dev-py2.7-macosx-10.8-intel.egg
> Processing dependencies for scikit-image==0.8dev
> Finished processing dependencies for scikit-image==0.8dev
>
> $ python
> Python 2.7.2 (default, Jun 20 2012, 16:23:33)
> [GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on
> darwin
> >>> import skimage
> >>> skimage.__version__
> '0.8dev'
> >>> import skimage.filter.rank as rank
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "skimage/filter/__init__.py", line 2, in <module>
>     from .ctmf import median_filter
>   File "skimage/filter/ctmf.py", line 15, in <module>
>     from . import _ctmf
> ImportError: cannot import name _ctmf
>
> Best,
>
> Parand
>

Hi Parand,

If those commands are exactly as you copied them above, it looks like
you're running the python interpreter from within the root scikit-image
directory. Since python prepends the path of the working directory to the
python path, you're actually importing the skimage package from that
directory---not the one you just installed (i.e. the one in site-packages).
You can check which you're running with:

    python -c 'import skimage; print skimage.__file__'

If you move up one directory and then start the python interpreter, does
the rank import work?

Best,
-Tony
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121214/3e61568f/attachment.html>

From hannesschoenberger at gmail.com  Fri Dec 14 08:37:43 2012
From: hannesschoenberger at gmail.com (=?windows-1252?Q?Sch=F6nberger_Johannes?=)
Date: Fri, 14 Dec 2012 14:37:43 +0100
Subject: import speedup
In-Reply-To: <72c15392-9d66-4153-9f26-8c7b2b06c6c4@googlegroups.com>
References: <72c15392-9d66-4153-9f26-8c7b2b06c6c4@googlegroups.com>
Message-ID: <4063C67F-BC23-4794-818B-29EC977C47F3@gmail.com>

Good catch! Another approach would be to rewrite and rename `_setup_test` to `test` and either delete the 'test_verbose' function or write it as `test_verbose = functools.partial(test, verbose=True)` to ged rid of the rather complex setup/lambda routine.

Would you add a PR for this, please? I could do it as well, if you don't want?

Johannes Sch?nberger

Am 14.12.2012 um 04:42 schrieb Steven Silvester <steven.silvester at gmail.com>:

> Hey all, I noticed that loading skimage seemed to take a bit longer than I'd like, so I profiled it.  On my machine, it takes 1.6 seconds to import skimage, 0.4 of which was from numpy, and 1.2 of which was from loading nose in skimage/__init__.py.  This simple patch brings my import time down to ~0.4 seconds, since it only imports nose when the test function is called.
> 
> diff --git a/skimage/__init__.py b/skimage/__init__.py
> index 1ac121b..f3e5e88 100644
> --- a/skimage/__init__.py
> +++ b/skimage/__init__.py
> @@ -84,8 +84,9 @@ def _setup_test(verbose=False):
>          return f
>  
>  
> -test = _setup_test()
> -test_verbose = _setup_test(verbose=True)
> +test = lambda : _setup_test()()
> +test_verbose = lambda : _setup_test(verbose=True)()
> +test_verbose.__doc__ = test.__doc__ = 'Invoke the skimage test suite.'
>  
>  
>  def get_log(name=None):
> 
> 
> -- 
>  
>  



From darugar at gmail.com  Sat Dec 15 01:18:54 2012
From: darugar at gmail.com (Parand Darugar)
Date: Fri, 14 Dec 2012 22:18:54 -0800 (PST)
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <CAEym_Hom=Qzx94a+sB7NyTmx5f1i7m1RZB=+1rPfYVkj87gb9A@mail.gmail.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com>
 <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com> <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>
 <66cc4b6d-2942-416a-a37a-d8fa196ce5df@googlegroups.com>
 <CAEym_Hom=Qzx94a+sB7NyTmx5f1i7m1RZB=+1rPfYVkj87gb9A@mail.gmail.com>
Message-ID: <e2a04e50-2345-4fff-b11e-ff8dcc8106a9@googlegroups.com>

Hi Tony,

You're absolutely right, that was the issue. Thanks very much.

Now to learn how to use scikit-image :-)

Best,

Parand

On Friday, December 14, 2012 11:37:32 AM UTC-8, Tony S Yu wrote:
>
>
>
> On Fri, Dec 14, 2012 at 1:31 PM, Parand Darugar <dar... at gmail.com<javascript:>
> > wrote:
>
>> Hi Tony,
>>
>> Installation steps:
>>
>> This is on OS X 10.8.2, Python 2.7.2:
>>
>> - I setup a virtualenv and activated that virtual env.
>> - I cloned the scikit-image git repository
>> - I installed:
>>
>> $ python ./setup.py install
>> ...
>> Installed 
>> /Users/parand/Projects/Receipts/pyenv/lib/python2.7/site-packages/scikit_image-0.8dev-py2.7-macosx-10.8-intel.egg
>> Processing dependencies for scikit-image==0.8dev
>> Finished processing dependencies for scikit-image==0.8dev
>>
>> $ python
>> Python 2.7.2 (default, Jun 20 2012, 16:23:33) 
>> [GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on 
>> darwin
>> >>> import skimage
>> >>> skimage.__version__
>> '0.8dev'
>> >>> import skimage.filter.rank as rank
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File "skimage/filter/__init__.py", line 2, in <module>
>>     from .ctmf import median_filter
>>   File "skimage/filter/ctmf.py", line 15, in <module>
>>     from . import _ctmf
>> ImportError: cannot import name _ctmf
>>
>> Best,
>>
>> Parand
>>
>
> Hi Parand,
>
> If those commands are exactly as you copied them above, it looks like 
> you're running the python interpreter from within the root scikit-image 
> directory. Since python prepends the path of the working directory to the 
> python path, you're actually importing the skimage package from that 
> directory---not the one you just installed (i.e. the one in site-packages). 
> You can check which you're running with:
>
>     python -c 'import skimage; print skimage.__file__'
>
> If you move up one directory and then start the python interpreter, does 
> the rank import work?
>
> Best,
> -Tony
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121214/7ebfc68c/attachment.html>

From dkin at walla.co.il  Sat Dec 15 13:58:27 2012
From: dkin at walla.co.il (Dan)
Date: Sat, 15 Dec 2012 10:58:27 -0800 (PST)
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com> <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
 <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com>
Message-ID: <2d1ccb5f-88cc-4275-8cc8-ac322b7b63b6@googlegroups.com>

Dear Tony,

Thanks for the script.

I was running the script and I got this error:
Traceback (most recent call last):
  File "C:/Users/DK/PProjects/skimage_seg/scikit_seg.py", line 18, in 
<module>
    img_background = morph.reconstruction(img-h, img)
AttributeError: 'module' object has no attribute 'reconstruction'

Process finished with exit code 1

Any reason why?

Thanks a lot,
Dan
El lunes, 24 de septiembre de 2012 18:58:19 UTC-4, Tony S Yu escribi?:
>
>
>
> On Fri, Sep 21, 2012 at 8:46 PM, St?fan van der Walt <ste... at sun.ac.za<javascript:>
> > wrote:
>
>> On Wed, Sep 19, 2012 at 4:01 AM, ashz <ashz... at gmail.com <javascript:>> 
>> wrote:
>>
>> > Granulometry of Snowflakes:
>> > 
>> http://www.mathworks.com/products/image/examples.html?file=/products/demos/shipping/images/ipexsnow.html
>>
>> Tony, do you think the morphological reconstruction would work for
>> this?
>
>
> Yes and no. Morphological reconstruction (specifically, h-dome, a.k.a. 
> h-maxima or regional max) tries to enhance features (maxima) based on the 
> local region. So the h-dome of a dim snowflake and bright snowflake will 
> look similar if they have a similar peakiness. In the original example, dim 
> peaks are still much dimmer than the bright peaks, even after the adaptive 
> histogram equalization. 
>
> Also, the h-dome of an image will tend to remove the corona-like blurring 
> around the larger snowflakes since the middle is so much brighter than the 
> surrounding region. I've attached an image of the results, along with the 
> code to generate it (although you can't run it without the snowflakes 
> image, which I probably shouldn't email). You'll notice that dim peaks are 
> much brighter than in the example, and the large snowflakes are smaller 
> (because of suppression of the corona region). These differences alter the 
> intensity curve quite a bit (I'm not sure what the "right" output is, 
> though).
>  
>
>> Otherwise perhaps one of the segmentation algorithms.
>> Translating the example line-by-line is pretty easy, except that we do
>> not have adaptive histogram equalization implemented yet.
>>
>
> BTW, there's a pending PR to add adaptive histogram equalization<https://github.com/scikits-image/scikits-image/pull/242>. 
> (Although, I'm not sure how I feel about the large header file required for 
> that PR.)
>
> As for the original post about these Matlab examples: Thanks for bringing 
> this up, ashz! These are exactly the type of examples I'd like to see in 
> the user guide: Something that takes the user all the way from image 
> loading to data extraction. We'd probably want to write our own instead of 
> simply translating the Matlab examples. It'd be great if people on this 
> list could provide examples from their own research.
>
> Best,
> -Tony
>
>  
> [image: Inline image 1]
>
> # Code to generate image above
> # Note: this won't run without image from Matlab install:
> #     toolbox/images/imdemos/snowflakes.png
>
>
> from skimage import io
> from skimage import img_as_float
> import skimage.morphology as morph
> from skimage import exposure
> from scipy import ndimage
>
>
> # snowflake image from a Matlab install
> img = io.imread('snowflakes.png')
> # convert from uint8 to float since we'll be subtracting (prevent 
> underflow)
> orig = img_as_float(img)
>
> img = exposure.equalize(img)
> img = ndimage.gaussian_filter(img, 1)
>
> # look for regional maxima greater than surrounding regions by h
> h = 0.2
> img_background = morph.reconstruction(img-h, img)
> img_hdome = img - img_background
> img = exposure.rescale_intensity(img_hdome)
>
> io.imshow(img)
> # io.imsave('snowflakes_enhanced.png', img)
> io.show()
>  
>  
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121215/b424647e/attachment.html>

From dkin at walla.co.il  Sat Dec 15 18:45:29 2012
From: dkin at walla.co.il (Dan)
Date: Sat, 15 Dec 2012 15:45:29 -0800 (PST)
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <CAEym_HrK1=vJqStXFwpA3y96DkvftL-nXwHVNckDWRwhu-ncDw@mail.gmail.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
 <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
 <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com> <2d1ccb5f-88cc-4275-8cc8-ac322b7b63b6@googlegroups.com>
 <CAEym_HrK1=vJqStXFwpA3y96DkvftL-nXwHVNckDWRwhu-ncDw@mail.gmail.com>
Message-ID: <c1f2d03c-e7ec-4b71-ad5d-0b94b9373967@googlegroups.com>

Hi,

Thanks for the rapid respnse, I am using 0.7.2 on windows.

The error is now:
 Traceback (most recent call last):
  File "C:/Users/DK/PProjects/skimage_seg/scikit_seg.py", line 3, in 
<module>
    import skimage.morphology as morph
  File "C:\Python27\lib\site-packages\skimage\morphology\__init__.py", line 
7, in <module>
    from ._skeletonize import skeletonize, medial_axis
ImportError: cannot import name skeletonize

Any idea why?.

Thanks



El s?bado, 15 de diciembre de 2012 16:24:31 UTC-5, Tony S Yu escribi?:
>
> On Sat, Dec 15, 2012 at 1:58 PM, Dan <dk... at walla.co.il <javascript:>>wrote:
>
>> Dear Tony,
>>
>> Thanks for the script.
>>
>> I was running the script and I got this error:
>> Traceback (most recent call last):
>>   File "C:/Users/DK/PProjects/skimage_seg/scikit_seg.py", line 18, in 
>> <module>
>>     img_background = morph.reconstruction(img-h, img)
>> AttributeError: 'module' object has no attribute 'reconstruction'
>>
>> Process finished with exit code 1
>>
>> Any reason why?
>>
>> Thanks a lot,
>> Dan
>>
>
> Hi Dan,
>
> Which version of scikit-image are you running? You'll need at least 0.7 
> (the latest stable release). You can check the version with the following 
> shell command:
>
>     $ python -c "import skimage; print skimage.__version__"
>
> -Tony 
>
> El lunes, 24 de septiembre de 2012 18:58:19 UTC-4, Tony S Yu escribi?:
>>>
>>>
>>>
>>> On Fri, Sep 21, 2012 at 8:46 PM, St?fan van der Walt <ste... at sun.ac.za>wrote:
>>>
>>> On Wed, Sep 19, 2012 at 4:01 AM, ashz <ashz... at gmail.com> wrote:
>>>>
>>>> > Granulometry of Snowflakes:
>>>> > http://www.mathworks.com/**products/image/examples.html?**
>>>> file=/products/demos/shipping/**images/ipexsnow.html<http://www.mathworks.com/products/image/examples.html?file=/products/demos/shipping/images/ipexsnow.html>
>>>>
>>>> Tony, do you think the morphological reconstruction would work for
>>>> this?
>>>
>>>
>>> Yes and no. Morphological reconstruction (specifically, h-dome, a.k.a. 
>>> h-maxima or regional max) tries to enhance features (maxima) based on the 
>>> local region. So the h-dome of a dim snowflake and bright snowflake will 
>>> look similar if they have a similar peakiness. In the original example, dim 
>>> peaks are still much dimmer than the bright peaks, even after the adaptive 
>>> histogram equalization. 
>>>
>>> Also, the h-dome of an image will tend to remove the corona-like 
>>> blurring around the larger snowflakes since the middle is so much brighter 
>>> than the surrounding region. I've attached an image of the results, along 
>>> with the code to generate it (although you can't run it without the 
>>> snowflakes image, which I probably shouldn't email). You'll notice that dim 
>>> peaks are much brighter than in the example, and the large snowflakes are 
>>> smaller (because of suppression of the corona region). These differences 
>>> alter the intensity curve quite a bit (I'm not sure what the "right" output 
>>> is, though).
>>>  
>>>
>>>> Otherwise perhaps one of the segmentation algorithms.
>>>> Translating the example line-by-line is pretty easy, except that we do
>>>> not have adaptive histogram equalization implemented yet.
>>>>
>>>
>>> BTW, there's a pending PR to add adaptive histogram equalization<https://github.com/scikits-image/scikits-image/pull/242>. 
>>> (Although, I'm not sure how I feel about the large header file required for 
>>> that PR.)
>>>
>>> As for the original post about these Matlab examples: Thanks for 
>>> bringing this up, ashz! These are exactly the type of examples I'd like to 
>>> see in the user guide: Something that takes the user all the way from image 
>>> loading to data extraction. We'd probably want to write our own instead of 
>>> simply translating the Matlab examples. It'd be great if people on this 
>>> list could provide examples from their own research.
>>>
>>> Best,
>>> -Tony
>>>
>>>  
>>> [image: Inline image 1]
>>>
>>> # Code to generate image above
>>> # Note: this won't run without image from Matlab install:
>>> #     toolbox/images/imdemos/**snowflakes.png
>>>
>>>
>>> from skimage import io
>>> from skimage import img_as_float
>>> import skimage.morphology as morph
>>> from skimage import exposure
>>> from scipy import ndimage
>>>
>>>
>>> # snowflake image from a Matlab install
>>> img = io.imread('snowflakes.png')
>>> # convert from uint8 to float since we'll be subtracting (prevent 
>>> underflow)
>>> orig = img_as_float(img)
>>>
>>> img = exposure.equalize(img)
>>> img = ndimage.gaussian_filter(img, 1)
>>>
>>> # look for regional maxima greater than surrounding regions by h
>>> h = 0.2
>>> img_background = morph.reconstruction(img-h, img)
>>> img_hdome = img - img_background
>>> img = exposure.rescale_intensity(**img_hdome)
>>>
>>> io.imshow(img)
>>>  # io.imsave('snowflakes_**enhanced.png', img)
>>> io.show()
>>>  
>>>  
>>>
>>>  -- 
>>  
>>  
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121215/fa12bec6/attachment.html>

From tsyu80 at gmail.com  Sat Dec 15 16:24:31 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sat, 15 Dec 2012 16:24:31 -0500
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <2d1ccb5f-88cc-4275-8cc8-ac322b7b63b6@googlegroups.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
 <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
 <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com> <2d1ccb5f-88cc-4275-8cc8-ac322b7b63b6@googlegroups.com>
Message-ID: <CAEym_HrK1=vJqStXFwpA3y96DkvftL-nXwHVNckDWRwhu-ncDw@mail.gmail.com>

On Sat, Dec 15, 2012 at 1:58 PM, Dan <dkin at walla.co.il> wrote:

> Dear Tony,
>
> Thanks for the script.
>
> I was running the script and I got this error:
> Traceback (most recent call last):
>   File "C:/Users/DK/PProjects/skimage_seg/scikit_seg.py", line 18, in
> <module>
>     img_background = morph.reconstruction(img-h, img)
> AttributeError: 'module' object has no attribute 'reconstruction'
>
> Process finished with exit code 1
>
> Any reason why?
>
> Thanks a lot,
> Dan
>

Hi Dan,

Which version of scikit-image are you running? You'll need at least 0.7
(the latest stable release). You can check the version with the following
shell command:

    $ python -c "import skimage; print skimage.__version__"

-Tony

El lunes, 24 de septiembre de 2012 18:58:19 UTC-4, Tony S Yu escribi?:
>>
>>
>>
>> On Fri, Sep 21, 2012 at 8:46 PM, St?fan van der Walt <ste... at sun.ac.za>wrote:
>>
>> On Wed, Sep 19, 2012 at 4:01 AM, ashz <ashz... at gmail.com> wrote:
>>>
>>> > Granulometry of Snowflakes:
>>> > http://www.mathworks.com/**products/image/examples.html?**
>>> file=/products/demos/shipping/**images/ipexsnow.html<http://www.mathworks.com/products/image/examples.html?file=/products/demos/shipping/images/ipexsnow.html>
>>>
>>> Tony, do you think the morphological reconstruction would work for
>>> this?
>>
>>
>> Yes and no. Morphological reconstruction (specifically, h-dome, a.k.a.
>> h-maxima or regional max) tries to enhance features (maxima) based on the
>> local region. So the h-dome of a dim snowflake and bright snowflake will
>> look similar if they have a similar peakiness. In the original example, dim
>> peaks are still much dimmer than the bright peaks, even after the adaptive
>> histogram equalization.
>>
>> Also, the h-dome of an image will tend to remove the corona-like blurring
>> around the larger snowflakes since the middle is so much brighter than the
>> surrounding region. I've attached an image of the results, along with the
>> code to generate it (although you can't run it without the snowflakes
>> image, which I probably shouldn't email). You'll notice that dim peaks are
>> much brighter than in the example, and the large snowflakes are smaller
>> (because of suppression of the corona region). These differences alter the
>> intensity curve quite a bit (I'm not sure what the "right" output is,
>> though).
>>
>>
>>> Otherwise perhaps one of the segmentation algorithms.
>>> Translating the example line-by-line is pretty easy, except that we do
>>> not have adaptive histogram equalization implemented yet.
>>>
>>
>> BTW, there's a pending PR to add adaptive histogram equalization<https://github.com/scikits-image/scikits-image/pull/242>.
>> (Although, I'm not sure how I feel about the large header file required for
>> that PR.)
>>
>> As for the original post about these Matlab examples: Thanks for bringing
>> this up, ashz! These are exactly the type of examples I'd like to see in
>> the user guide: Something that takes the user all the way from image
>> loading to data extraction. We'd probably want to write our own instead of
>> simply translating the Matlab examples. It'd be great if people on this
>> list could provide examples from their own research.
>>
>> Best,
>> -Tony
>>
>>
>> [image: Inline image 1]
>>
>> # Code to generate image above
>> # Note: this won't run without image from Matlab install:
>> #     toolbox/images/imdemos/**snowflakes.png
>>
>>
>> from skimage import io
>> from skimage import img_as_float
>> import skimage.morphology as morph
>> from skimage import exposure
>> from scipy import ndimage
>>
>>
>> # snowflake image from a Matlab install
>> img = io.imread('snowflakes.png')
>> # convert from uint8 to float since we'll be subtracting (prevent
>> underflow)
>> orig = img_as_float(img)
>>
>> img = exposure.equalize(img)
>> img = ndimage.gaussian_filter(img, 1)
>>
>> # look for regional maxima greater than surrounding regions by h
>> h = 0.2
>> img_background = morph.reconstruction(img-h, img)
>> img_hdome = img - img_background
>> img = exposure.rescale_intensity(**img_hdome)
>>
>> io.imshow(img)
>>  # io.imsave('snowflakes_**enhanced.png', img)
>> io.show()
>>
>>
>>
>>  --
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121215/bcecb4f5/attachment.html>

From dkin at walla.co.il  Sun Dec 16 03:57:48 2012
From: dkin at walla.co.il (Dan)
Date: Sun, 16 Dec 2012 00:57:48 -0800 (PST)
Subject: High order statistics/Gary level runlength matrices statistics
In-Reply-To: <d8412b4c-2606-42a2-93d3-2155dde1792c@googlegroups.com>
References: <d8412b4c-2606-42a2-93d3-2155dde1792c@googlegroups.com>
Message-ID: <e18e8310-75ad-4da5-81fb-9a26f45111d1@googlegroups.com>

Is this interesting option going to be implmented in the future release?



El mi?rcoles, 28 de noviembre de 2012 05:21:35 UTC-5, Dan escribi?:
>
> Dear all,
>
> Is Scikit-image able to provide High order statistics/Gary level runlength 
> matrices statistics values(e.g., Short Run Emphasis, Long Run Emphasis, 
> Gray-Level Nonuniformity, Run Length Nonuniformity, Run Percentage, etc)?.
>
> Is there a way to calculate it using Scikit-image?
>
> Thanks a lot in advance.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121216/84994ae9/attachment.html>

From dkin at walla.co.il  Sun Dec 16 10:36:13 2012
From: dkin at walla.co.il (Dan)
Date: Sun, 16 Dec 2012 07:36:13 -0800 (PST)
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <CAEym_Hoo8P3tsPHwS35NoN6Z-=TtcTwkmvC306WuOOi4XBxXUg@mail.gmail.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
 <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
 <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com>
 <2d1ccb5f-88cc-4275-8cc8-ac322b7b63b6@googlegroups.com> <CAEym_HrK1=vJqStXFwpA3y96DkvftL-nXwHVNckDWRwhu-ncDw@mail.gmail.com>
 <c1f2d03c-e7ec-4b71-ad5d-0b94b9373967@googlegroups.com>
 <CAEym_Hoo8P3tsPHwS35NoN6Z-=TtcTwkmvC306WuOOi4XBxXUg@mail.gmail.com>
Message-ID: <ca3b5c65-0470-44dc-b721-97129a12163c@googlegroups.com>

Hi,

The output:
Python 2.7.3 (default, Apr 10 2012, 23:31:26) [MSC v.1500 32 bit (Intel)] 
on win32
Type "copyright", "credits" or "license()" for more information.
>>> import skimage
>>> print skimage.__version__
0.7.2
>>> print skimage.__file__
C:\Python27\lib\site-packages\skimage\__init__.pyc
>>> 

Thanks

El domingo, 16 de diciembre de 2012 09:41:35 UTC-5, Tony S Yu escribi?:
>
> On Sat, Dec 15, 2012 at 6:45 PM, Dan <dk... at walla.co.il <javascript:>>wrote:
>
>> Hi,
>>
>> Thanks for the rapid respnse, I am using 0.7.2 on windows.
>>
>> The error is now:
>>
>>  Traceback (most recent call last):
>>   File "C:/Users/DK/PProjects/skimage_seg/scikit_seg.py", line 3, in 
>> <module>
>>     import skimage.morphology as morph
>>   File "C:\Python27\lib\site-packages\skimage\morphology\__init__.py", 
>> line 7, in <module>
>>     from ._skeletonize import skeletonize, medial_axis
>> ImportError: cannot import name skeletonize
>>
>> Any idea why?.
>>
>> Thanks
>>
>
>
> Hi Dan,
>
> How did you install scikit-image? Also, what's the output of the following?
>
>
> import skimage
> print skimage.__version__
> print skimage.__file__
>
>
> -Tony
>
>
>
>> El s?bado, 15 de diciembre de 2012 16:24:31 UTC-5, Tony S Yu escribi?:
>>
>>> On Sat, Dec 15, 2012 at 1:58 PM, Dan <dk... at walla.co.il> wrote:
>>>
>>>> Dear Tony,
>>>>
>>>> Thanks for the script.
>>>>
>>>> I was running the script and I got this error:
>>>> Traceback (most recent call last):
>>>>   File "C:/Users/DK/PProjects/**skimage_seg/scikit_seg.py", line 18, 
>>>> in <module>
>>>>     img_background = morph.reconstruction(img-h, img)
>>>> AttributeError: 'module' object has no attribute 'reconstruction'
>>>>
>>>> Process finished with exit code 1
>>>>
>>>> Any reason why?
>>>>
>>>> Thanks a lot,
>>>> Dan
>>>>
>>>
>>> Hi Dan,
>>>
>>> Which version of scikit-image are you running? You'll need at least 0.7 
>>> (the latest stable release). You can check the version with the following 
>>> shell command:
>>>
>>>     $ python -c "import skimage; print skimage.__version__"
>>>
>>> -Tony 
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121216/9ccf9342/attachment.html>

From dkin at walla.co.il  Sun Dec 16 10:41:43 2012
From: dkin at walla.co.il (Dan)
Date: Sun, 16 Dec 2012 07:41:43 -0800 (PST)
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <ca3b5c65-0470-44dc-b721-97129a12163c@googlegroups.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
 <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
 <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com>
 <2d1ccb5f-88cc-4275-8cc8-ac322b7b63b6@googlegroups.com> <CAEym_HrK1=vJqStXFwpA3y96DkvftL-nXwHVNckDWRwhu-ncDw@mail.gmail.com>
 <c1f2d03c-e7ec-4b71-ad5d-0b94b9373967@googlegroups.com>
 <CAEym_Hoo8P3tsPHwS35NoN6Z-=TtcTwkmvC306WuOOi4XBxXUg@mail.gmail.com>
 <ca3b5c65-0470-44dc-b721-97129a12163c@googlegroups.com>
Message-ID: <b8617deb-4080-4c0b-8333-4ef1fa8e71f0@googlegroups.com>

Hi,

I installed Windows binaries (kindly provided by Christoph Gohlke)- file 
name:scikit-image-0.7.2.win32-py2.7.?exe

Thanks

El domingo, 16 de diciembre de 2012 10:36:13 UTC-5, Dan escribi?:
>
> Hi,
>
> The output:
> Python 2.7.3 (default, Apr 10 2012, 23:31:26) [MSC v.1500 32 bit (Intel)] 
> on win32
> Type "copyright", "credits" or "license()" for more information.
> >>> import skimage
> >>> print skimage.__version__
> 0.7.2
> >>> print skimage.__file__
> C:\Python27\lib\site-packages\skimage\__init__.pyc
> >>> 
>
> Thanks
>
> El domingo, 16 de diciembre de 2012 09:41:35 UTC-5, Tony S Yu escribi?:
>>
>> On Sat, Dec 15, 2012 at 6:45 PM, Dan <dk... at walla.co.il> wrote:
>>
>>> Hi,
>>>
>>> Thanks for the rapid respnse, I am using 0.7.2 on windows.
>>>
>>> The error is now:
>>>
>>>  Traceback (most recent call last):
>>>   File "C:/Users/DK/PProjects/skimage_seg/scikit_seg.py", line 3, in 
>>> <module>
>>>     import skimage.morphology as morph
>>>   File "C:\Python27\lib\site-packages\skimage\morphology\__init__.py", 
>>> line 7, in <module>
>>>     from ._skeletonize import skeletonize, medial_axis
>>> ImportError: cannot import name skeletonize
>>>
>>> Any idea why?.
>>>
>>> Thanks
>>>
>>
>>
>> Hi Dan,
>>
>> How did you install scikit-image? Also, what's the output of the 
>> following?
>>
>>
>> import skimage
>> print skimage.__version__
>> print skimage.__file__
>>
>>
>> -Tony
>>
>>
>>
>>> El s?bado, 15 de diciembre de 2012 16:24:31 UTC-5, Tony S Yu escribi?:
>>>
>>>> On Sat, Dec 15, 2012 at 1:58 PM, Dan <dk... at walla.co.il> wrote:
>>>>
>>>>> Dear Tony,
>>>>>
>>>>> Thanks for the script.
>>>>>
>>>>> I was running the script and I got this error:
>>>>> Traceback (most recent call last):
>>>>>   File "C:/Users/DK/PProjects/**skimage_seg/scikit_seg.py", line 18, 
>>>>> in <module>
>>>>>     img_background = morph.reconstruction(img-h, img)
>>>>> AttributeError: 'module' object has no attribute 'reconstruction'
>>>>>
>>>>> Process finished with exit code 1
>>>>>
>>>>> Any reason why?
>>>>>
>>>>> Thanks a lot,
>>>>> Dan
>>>>>
>>>>
>>>> Hi Dan,
>>>>
>>>> Which version of scikit-image are you running? You'll need at least 0.7 
>>>> (the latest stable release). You can check the version with the following 
>>>> shell command:
>>>>
>>>>     $ python -c "import skimage; print skimage.__version__"
>>>>
>>>> -Tony 
>>>>
>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121216/f31dbc3e/attachment.html>

From tsyu80 at gmail.com  Sun Dec 16 09:41:35 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 16 Dec 2012 09:41:35 -0500
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <c1f2d03c-e7ec-4b71-ad5d-0b94b9373967@googlegroups.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
 <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
 <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com>
 <2d1ccb5f-88cc-4275-8cc8-ac322b7b63b6@googlegroups.com> <CAEym_HrK1=vJqStXFwpA3y96DkvftL-nXwHVNckDWRwhu-ncDw@mail.gmail.com>
 <c1f2d03c-e7ec-4b71-ad5d-0b94b9373967@googlegroups.com>
Message-ID: <CAEym_Hoo8P3tsPHwS35NoN6Z-=TtcTwkmvC306WuOOi4XBxXUg@mail.gmail.com>

On Sat, Dec 15, 2012 at 6:45 PM, Dan <dkin at walla.co.il> wrote:

> Hi,
>
> Thanks for the rapid respnse, I am using 0.7.2 on windows.
>
> The error is now:
>
>  Traceback (most recent call last):
>   File "C:/Users/DK/PProjects/skimage_seg/scikit_seg.py", line 3, in
> <module>
>     import skimage.morphology as morph
>   File "C:\Python27\lib\site-packages\skimage\morphology\__init__.py",
> line 7, in <module>
>     from ._skeletonize import skeletonize, medial_axis
> ImportError: cannot import name skeletonize
>
> Any idea why?.
>
> Thanks
>


Hi Dan,

How did you install scikit-image? Also, what's the output of the following?


import skimage
print skimage.__version__
print skimage.__file__


-Tony



> El s?bado, 15 de diciembre de 2012 16:24:31 UTC-5, Tony S Yu escribi?:
>
>> On Sat, Dec 15, 2012 at 1:58 PM, Dan <dk... at walla.co.il> wrote:
>>
>>> Dear Tony,
>>>
>>> Thanks for the script.
>>>
>>> I was running the script and I got this error:
>>> Traceback (most recent call last):
>>>   File "C:/Users/DK/PProjects/**skimage_seg/scikit_seg.py", line 18, in
>>> <module>
>>>     img_background = morph.reconstruction(img-h, img)
>>> AttributeError: 'module' object has no attribute 'reconstruction'
>>>
>>> Process finished with exit code 1
>>>
>>> Any reason why?
>>>
>>> Thanks a lot,
>>> Dan
>>>
>>
>> Hi Dan,
>>
>> Which version of scikit-image are you running? You'll need at least 0.7
>> (the latest stable release). You can check the version with the following
>> shell command:
>>
>>     $ python -c "import skimage; print skimage.__version__"
>>
>> -Tony
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121216/bc03f575/attachment.html>

From darugar at gmail.com  Sun Dec 16 19:09:47 2012
From: darugar at gmail.com (Parand Darugar)
Date: Sun, 16 Dec 2012 16:09:47 -0800 (PST)
Subject: Filter out large segments
Message-ID: <4ab38a9b-8fa3-437f-a199-d79d457e2301@googlegroups.com>

Hello,

Not sure if it's appropriate to ask algorithm questions on this mailing 
list, please let me know if it's not.

I'd like to filter out large contiguous regions out of my image - I only 
care about smaller items. Following the Image Segmentation 
example/tutorial, I'm able to find and label the large segments using an 
Otsu threshold and ndimage.label.

Now I'd like to replace these large segments with "white", where "white" is 
the max value find in my grayscale image (basically I'd like to blank them 
out).

I'm not quite following how this is done in the tutorial:

>>> label_objects, nb_labels = ndimage.label(fill_coins)
>>> sizes = np.bincount(label_objects.ravel())
>>> mask_sizes = sizes > 20
>>> mask_sizes[0] = 0
>>> coins_cleaned = mask_sizes[label_objects]

How does the coins_cleaned = mask_sizes[label_objects] line clean the 
image? 

Generally speaking, given the labeled segments (label_objects from the 
tutorial), how would I apply operations to the original image - for 
example: set all of the pixels in "image" that are parts of objects labeled 
3 and 9 to 0.577 .

Also, how do I get smarter about how the system works so I don't ask 
elementary questions? Is there a good high level tutorial that'll 
familiarize me with the computation model for skimage / ndimage ?

Best,

Parand
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121216/d66eb5b6/attachment.html>

From tsyu80 at gmail.com  Sun Dec 16 21:46:08 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 16 Dec 2012 21:46:08 -0500
Subject: Filter out large segments
In-Reply-To: <4ab38a9b-8fa3-437f-a199-d79d457e2301@googlegroups.com>
References: <4ab38a9b-8fa3-437f-a199-d79d457e2301@googlegroups.com>
Message-ID: <CAEym_HqSkqjUjnEOYaXPnCxj2H=zJ=ZNXzS8ogk_DiWVVwkbgw@mail.gmail.com>

Hi again,

On Sun, Dec 16, 2012 at 7:09 PM, Parand Darugar <darugar at gmail.com> wrote:

> Hello,
>
> Not sure if it's appropriate to ask algorithm questions on this mailing
> list, please let me know if it's not.
>

Algorithm questions are definitely welcome.


> I'd like to filter out large contiguous regions out of my image - I only
> care about smaller items. Following the Image Segmentation
> example/tutorial, I'm able to find and label the large segments using an
> Otsu threshold and ndimage.label.
>
> Now I'd like to replace these large segments with "white", where "white"
> is the max value find in my grayscale image (basically I'd like to blank
> them out).
>
> I'm not quite following how this is done in the tutorial:
>
> >>> label_objects, nb_labels = ndimage.label(fill_coins)
> >>> sizes = np.bincount(label_objects.ravel())
> >>> mask_sizes = sizes > 20
> >>> mask_sizes[0] = 0
> >>> coins_cleaned = mask_sizes[label_objects]
>
> How does the coins_cleaned = mask_sizes[label_objects] line clean the
> image?
>

In case you didn't follow the `bincount` part: The `sizes` array is a count
of frequency of each label; so large labeled regions would have a large
size. The index is matched to the integer label: the count for label `i` is
stored in `sizes[i]`.

`mask_sizes` just looks for all labeled region larger than 20 pixels and
stores a boolean array (i.e. mask). So if the region labeled `i` has more
than 20 pixels then `mask_sizes[i]` is True. Also, `i = 0` values are set
to 0 because `i = 0` is reserved as the background label.

Based on your question, you probably understood all that, but I just wanted
to make sure we're on the same page. Now, the line that you actually asked
about is a bit of a numpy trick: It uses `label_objects` to pick values
from `mask_sizes`. A pixel labeled `i` (in `label_objects`) will grab the
value in `mask_sizes[i]` (i.e. True or False); that value will then get
placed in the output array at the same array position as the pixel in
`label_objects`.

That explanation was a bit confusing. Perhaps a short example will help:


>>> import numpy as np
>>> values = np.array([0, 0, 0, 1]) # stand-in for `mask_sizes`
>>> picker = np.array([[0, 1, 2, 3],
...                    [3, 0, 1, 2],
...                    [2, 3, 0, 1],
...                    [1, 2, 3, 0]])  # stand-in for `label_objects`
 >>> print values[picker]
[[0 0 0 1]
 [1 0 0 0]
 [0 1 0 0]
 [0 0 1 0]]


All the values in the picker labeled 3 are set to 1 in the output because
that was the value at `values[3]`. All other values were 0.



> Generally speaking, given the labeled segments (label_objects from the
> tutorial), how would I apply operations to the original image - for
> example: set all of the pixels in "image" that are parts of objects labeled
> 3 and 9 to 0.577 .
>

Something like this should work:


>>> mask_low = image < 3
>>> mask_high = image > 9
>>> image[mask_low & mask_high] = 0.577


Also, how do I get smarter about how the system works so I don't ask
> elementary questions? Is there a good high level tutorial that'll
> familiarize me with the computation model for skimage / ndimage ?
>

Well, I think these questions are more focused on numpy, which forms the
core of skimage. There are tons of numpy tutorials out there, but I don't
have a particular favorite. Someone on the numpy mailing list pointed to
the following tutorial:

http://scipy-lectures.github.com/intro/numpy/index.html

So that might be worth a look.

Best,
-Tony


>
> Best,
>
> Parand
>
> --
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121216/68b0e102/attachment.html>

From tsyu80 at gmail.com  Sun Dec 16 23:23:00 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Sun, 16 Dec 2012 23:23:00 -0500
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <b8617deb-4080-4c0b-8333-4ef1fa8e71f0@googlegroups.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
 <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
 <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com>
 <2d1ccb5f-88cc-4275-8cc8-ac322b7b63b6@googlegroups.com> <CAEym_HrK1=vJqStXFwpA3y96DkvftL-nXwHVNckDWRwhu-ncDw@mail.gmail.com>
 <c1f2d03c-e7ec-4b71-ad5d-0b94b9373967@googlegroups.com> <CAEym_Hoo8P3tsPHwS35NoN6Z-=TtcTwkmvC306WuOOi4XBxXUg@mail.gmail.com>
 <ca3b5c65-0470-44dc-b721-97129a12163c@googlegroups.com> <b8617deb-4080-4c0b-8333-4ef1fa8e71f0@googlegroups.com>
Message-ID: <CAEym_HpqAhvMfsD2CrLHnmJr6yPFwkMc6dAXKZW5f2wp21wH-Q@mail.gmail.com>

On Sun, Dec 16, 2012 at 10:41 AM, Dan <dkin at walla.co.il> wrote:

> Hi,
>
> I installed Windows binaries (kindly provided by Christoph Gohlke)- file
> name:scikit-image-0.7.2.win32-py2.7.exe
>
> Thanks
>
> El domingo, 16 de diciembre de 2012 10:36:13 UTC-5, Dan escribi?:
>
>> Hi,
>>
>> The output:
>> Python 2.7.3 (default, Apr 10 2012, 23:31:26) [MSC v.1500 32 bit (Intel)]
>> on win32
>> Type "copyright", "credits" or "license()" for more information.
>> >>> import skimage
>> >>> print skimage.__version__
>> 0.7.2
>> >>> print skimage.__file__
>> C:\Python27\lib\site-packages\**skimage\__init__.pyc
>> >>>
>>
>> Thanks
>>
>

Hmm... that all looks good to me.

Maybe something went wrong during the install? This is bizarre, because
`_skeletonize` is a regular python file (not cython, so it's not a build
issue). If you look in

"C:\Python27\lib\site-**packages\skimage\morphology\"


is there a "_skeletonize.py" and does it like the
original<https://github.com/scikit-image/scikit-image/blob/v0.7.2/skimage/morphology/_skeletonize.py>
(i.e.
does it have a `skeletonize` function)?

-Tony


>> El domingo, 16 de diciembre de 2012 09:41:35 UTC-5, Tony S Yu escribi?:
>>>
>>> On Sat, Dec 15, 2012 at 6:45 PM, Dan <dk... at walla.co.il> wrote:
>>>
>>>> Hi,
>>>>
>>>> Thanks for the rapid respnse, I am using 0.7.2 on windows.
>>>>
>>>> The error is now:
>>>>
>>>>  Traceback (most recent call last):
>>>>   File "C:/Users/DK/PProjects/**skimage_seg/scikit_seg.py", line 3, in
>>>> <module>
>>>>     import skimage.morphology as morph
>>>>   File "C:\Python27\lib\site-**packages\skimage\morphology\__**init__.py",
>>>> line 7, in <module>
>>>>     from ._skeletonize import skeletonize, medial_axis
>>>> ImportError: cannot import name skeletonize
>>>>
>>>> Any idea why?.
>>>>
>>>> Thanks
>>>>
>>>
>>>
>>> Hi Dan,
>>>
>>> How did you install scikit-image? Also, what's the output of the
>>> following?
>>>
>>>
>>> import skimage
>>> print skimage.__version__
>>> print skimage.__file__
>>>
>>>
>>> -Tony
>>>
>>>
>>>
>>>> El s?bado, 15 de diciembre de 2012 16:24:31 UTC-5, Tony S Yu escribi?:
>>>>
>>>>> On Sat, Dec 15, 2012 at 1:58 PM, Dan <dk... at walla.co.il> wrote:
>>>>>
>>>>>> Dear Tony,
>>>>>>
>>>>>> Thanks for the script.
>>>>>>
>>>>>> I was running the script and I got this error:
>>>>>> Traceback (most recent call last):
>>>>>>   File "C:/Users/DK/PProjects/**skimage**_seg/scikit_seg.py", line
>>>>>> 18, in <module>
>>>>>>     img_background = morph.reconstruction(img-h, img)
>>>>>> AttributeError: 'module' object has no attribute 'reconstruction'
>>>>>>
>>>>>> Process finished with exit code 1
>>>>>>
>>>>>> Any reason why?
>>>>>>
>>>>>> Thanks a lot,
>>>>>> Dan
>>>>>>
>>>>>
>>>>> Hi Dan,
>>>>>
>>>>> Which version of scikit-image are you running? You'll need at least
>>>>> 0.7 (the latest stable release). You can check the version with the
>>>>> following shell command:
>>>>>
>>>>>     $ python -c "import skimage; print skimage.__version__"
>>>>>
>>>>> -Tony
>>>>>
>>>>  --
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121216/035c79fc/attachment.html>

From darugar at gmail.com  Mon Dec 17 02:50:26 2012
From: darugar at gmail.com (Parand Darugar)
Date: Sun, 16 Dec 2012 23:50:26 -0800 (PST)
Subject: import of skimage.morphology.selem.disk fails
Message-ID: <ed58a810-a3a1-47d7-8cb9-b566bed97c1f@googlegroups.com>

Hello,

"from skimage.morphology.selem import disk" fails with the message 
"ImportError: cannot import name convex_hull_image". Subsequent attempts to 
import result in message "ImportError: cannot import name _template".

System: Python 2.7.2 on OS X 1.8.2 , scikit-image latest version from git 

Installed via "python install setup.py" 

The install seemed to work fine - I can run most other scripts.

Full error log here:
http://pastebin.com/hD8ishuH

Any ideas?

Best,

Parand
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121216/20327bda/attachment.html>

From stefan at sun.ac.za  Mon Dec 17 03:03:51 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Mon, 17 Dec 2012 00:03:51 -0800
Subject: import of skimage.morphology.selem.disk fails
In-Reply-To: <ed58a810-a3a1-47d7-8cb9-b566bed97c1f@googlegroups.com>
References: <ed58a810-a3a1-47d7-8cb9-b566bed97c1f@googlegroups.com>
Message-ID: <CABDkGQmOTdGxREfs7JSdqSUNW_1v=7Sb3XdhhL-yrK9=tJRogg@mail.gmail.com>

Hi Prashand

On Sun, Dec 16, 2012 at 11:50 PM, Parand Darugar <darugar at gmail.com> wrote:
> "from skimage.morphology.selem import disk" fails with the message
> "ImportError: cannot import name convex_hull_image". Subsequent attempts to
> import result in message "ImportError: cannot import name _template".

No problems on this end.  Could you please send usyour build log?

Thanks
Stefan


From guillaume at mitotic-machine.org  Mon Dec 17 03:08:06 2012
From: guillaume at mitotic-machine.org (Guillaume Gay)
Date: Mon, 17 Dec 2012 09:08:06 +0100
Subject: import of skimage.morphology.selem.disk fails
In-Reply-To: <CABDkGQmOTdGxREfs7JSdqSUNW_1v=7Sb3XdhhL-yrK9=tJRogg@mail.gmail.com>
References: <ed58a810-a3a1-47d7-8cb9-b566bed97c1f@googlegroups.com> <CABDkGQmOTdGxREfs7JSdqSUNW_1v=7Sb3XdhhL-yrK9=tJRogg@mail.gmail.com>
Message-ID: <50CED2E6.9080902@mitotic-machine.org>

Le 17/12/2012 09:03, St?fan van der Walt a ?crit :
> Hi Prashand
>
> On Sun, Dec 16, 2012 at 11:50 PM, Parand Darugar <darugar at gmail.com> wrote:
>> "from skimage.morphology.selem import disk" fails with the message
>> "ImportError: cannot import name convex_hull_image". Subsequent attempts to
>> import result in message "ImportError: cannot import name _template".
> No problems on this end.  Could you please send usyour build log?
>
> Thanks
> Stefan
>
Hi

I had very similar import problems when I checked out the source from 
github last friday, that got sorted out by pulling it again sunday,
so maybe it is enough for you to update your repository and build again...

Guillaume


From jni.soma at gmail.com  Sun Dec 16 18:57:12 2012
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 17 Dec 2012 10:57:12 +1100
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <02582B6B-4C51-4153-894D-7E7B64DAB5ED@gmail.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com>
 <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com> <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>
 <CABDkGQ=Pd0T2qLdiLoPVv2JaLcAVrxWSVLW1umQB5GK+VUbe7Q@mail.gmail.com> <02582B6B-4C51-4153-894D-7E7B64DAB5ED@gmail.com>
Message-ID: <CA+JHcKS+9R3oOssOFva4L7Y_7eaEBVeFs=4nZYq0Cgnr_2CwXQ@mail.gmail.com>

On Sat, Dec 15, 2012 at 12:26 AM, Sch?nberger Johannes <
hannesschoenberger at gmail.com> wrote:

> Maybe the "Gallery" link in the navigation should point to the dev gallery
> and the "Documentation" link to the stable docs?
>

-1 for this one, as it could cause confusion if the gallery contains
examples that are not yet implemented in the stable release.

Perhaps you can add a "coming soon" link to the dev gallery?
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121217/1adcbb9d/attachment.html>

From tsyu80 at gmail.com  Mon Dec 17 16:37:35 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Mon, 17 Dec 2012 16:37:35 -0500
Subject: import of skimage.morphology.selem.disk fails
In-Reply-To: <50CED2E6.9080902@mitotic-machine.org>
References: <ed58a810-a3a1-47d7-8cb9-b566bed97c1f@googlegroups.com>
 <CABDkGQmOTdGxREfs7JSdqSUNW_1v=7Sb3XdhhL-yrK9=tJRogg@mail.gmail.com> <50CED2E6.9080902@mitotic-machine.org>
Message-ID: <CAEym_HoPAc=qHU=3PYdAfMK+8V1w4-Mj4w=NyHWOWrSzyP145w@mail.gmail.com>

On Mon, Dec 17, 2012 at 3:08 AM, Guillaume Gay <
guillaume at mitotic-machine.org> wrote:

> Le 17/12/2012 09:03, St?fan van der Walt a ?crit :
>
>  Hi Prashand
>>
>> On Sun, Dec 16, 2012 at 11:50 PM, Parand Darugar <darugar at gmail.com>
>> wrote:
>>
>>> "from skimage.morphology.selem import disk" fails with the message
>>> "ImportError: cannot import name convex_hull_image". Subsequent attempts
>>> to
>>> import result in message "ImportError: cannot import name _template".
>>>
>> No problems on this end.  Could you please send usyour build log?
>>
>> Thanks
>> Stefan
>>
>>  Hi
>
> I had very similar import problems when I checked out the source from
> github last friday, that got sorted out by pulling it again sunday,
> so maybe it is enough for you to update your repository and build again...
>
> Guillaume
>
>
I think Guillaume is correct here. The error looks like a circular import
that was fixed in PR
#394<https://github.com/scikit-image/scikit-image/pull/394>.
Does updating fix the issue?

-Tony
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121217/fb5300d9/attachment.html>

From darugar at gmail.com  Tue Dec 18 01:41:17 2012
From: darugar at gmail.com (Parand Darugar)
Date: Mon, 17 Dec 2012 22:41:17 -0800 (PST)
Subject: import of skimage.morphology.selem.disk fails
In-Reply-To: <CAEym_HoPAc=qHU=3PYdAfMK+8V1w4-Mj4w=NyHWOWrSzyP145w@mail.gmail.com>
References: <ed58a810-a3a1-47d7-8cb9-b566bed97c1f@googlegroups.com>
 <CABDkGQmOTdGxREfs7JSdqSUNW_1v=7Sb3XdhhL-yrK9=tJRogg@mail.gmail.com> <50CED2E6.9080902@mitotic-machine.org>
 <CAEym_HoPAc=qHU=3PYdAfMK+8V1w4-Mj4w=NyHWOWrSzyP145w@mail.gmail.com>
Message-ID: <9f4774a9-c9ec-4906-9e8b-3f36b577b023@googlegroups.com>

Yes indeed, a git pull and rebuild has fixed the issue. Much thanks!

Best,

Parand

On Monday, December 17, 2012 1:37:35 PM UTC-8, Tony S Yu wrote:
>
>
>
> On Mon, Dec 17, 2012 at 3:08 AM, Guillaume Gay <
> guil... at mitotic-machine.org <javascript:>> wrote:
>
>> Le 17/12/2012 09:03, St?fan van der Walt a ?crit :
>>
>>  Hi Prashand
>>>
>>> On Sun, Dec 16, 2012 at 11:50 PM, Parand Darugar <dar... at gmail.com<javascript:>> 
>>> wrote:
>>>
>>>> "from skimage.morphology.selem import disk" fails with the message
>>>> "ImportError: cannot import name convex_hull_image". Subsequent 
>>>> attempts to
>>>> import result in message "ImportError: cannot import name _template".
>>>>
>>> No problems on this end.  Could you please send usyour build log?
>>>
>>> Thanks
>>> Stefan
>>>
>>>  Hi
>>
>> I had very similar import problems when I checked out the source from 
>> github last friday, that got sorted out by pulling it again sunday,
>> so maybe it is enough for you to update your repository and build again...
>>
>> Guillaume
>>
>>
> I think Guillaume is correct here. The error looks like a circular import 
> that was fixed in PR #394<https://github.com/scikit-image/scikit-image/pull/394>. 
> Does updating fix the issue?
>
> -Tony
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121217/6f7994a9/attachment.html>

From dkin at walla.co.il  Thu Dec 20 03:33:39 2012
From: dkin at walla.co.il (Dan)
Date: Thu, 20 Dec 2012 00:33:39 -0800 (PST)
Subject: Segmentation and Granulometry with scikit-image
In-Reply-To: <CAEym_HpqAhvMfsD2CrLHnmJr6yPFwkMc6dAXKZW5f2wp21wH-Q@mail.gmail.com>
References: <4c817a46-75de-4ee7-b58e-1ddb08228126@googlegroups.com>
 <CABDkGQ=CRYyb=TcCXojOT-HZ6Ck8Rs=QAmFiD-sK+rNODmx+cw@mail.gmail.com>
 <CAEym_HqgidmfAab-zmYXyXnz-rz0D-xCB0zYu=ErChbyNmL-wQ@mail.gmail.com>
 <2d1ccb5f-88cc-4275-8cc8-ac322b7b63b6@googlegroups.com> <CAEym_HrK1=vJqStXFwpA3y96DkvftL-nXwHVNckDWRwhu-ncDw@mail.gmail.com>
 <c1f2d03c-e7ec-4b71-ad5d-0b94b9373967@googlegroups.com> <CAEym_Hoo8P3tsPHwS35NoN6Z-=TtcTwkmvC306WuOOi4XBxXUg@mail.gmail.com>
 <ca3b5c65-0470-44dc-b721-97129a12163c@googlegroups.com> <b8617deb-4080-4c0b-8333-4ef1fa8e71f0@googlegroups.com>
 <CAEym_HpqAhvMfsD2CrLHnmJr6yPFwkMc6dAXKZW5f2wp21wH-Q@mail.gmail.com>
Message-ID: <2c8ea1e1-61ab-4752-8b59-846c9bc12b4d@googlegroups.com>



El lunes, 17 de diciembre de 2012 05:23:00 UTC+1, Tony S Yu escribi?:
>
>
>
> On Sun, Dec 16, 2012 at 10:41 AM, Dan <dk... at walla.co.il <javascript:>>wrote:
>
>> Hi,
>>
>> I installed Windows binaries (kindly provided by Christoph Gohlke)- file 
>> name:scikit-image-0.7.2.win32-py2.7.exe
>>
>> Thanks
>>
>> El domingo, 16 de diciembre de 2012 10:36:13 UTC-5, Dan escribi?:
>>
>>> Hi,
>>>
>>> The output:
>>> Python 2.7.3 (default, Apr 10 2012, 23:31:26) [MSC v.1500 32 bit 
>>> (Intel)] on win32
>>> Type "copyright", "credits" or "license()" for more information.
>>> >>> import skimage
>>> >>> print skimage.__version__
>>> 0.7.2
>>> >>> print skimage.__file__
>>> C:\Python27\lib\site-packages\**skimage\__init__.pyc
>>> >>> 
>>>
>>> Thanks
>>>
>>
>
> Hmm... that all looks good to me.
>
> Maybe something went wrong during the install? This is bizarre, because 
> `_skeletonize` is a regular python file (not cython, so it's not a build 
> issue). If you look in 
>
> "C:\Python27\lib\site-**packages\skimage\morphology\"
>
>
> is there a "_skeletonize.py" and does it like the original<https://github.com/scikit-image/scikit-image/blob/v0.7.2/skimage/morphology/_skeletonize.py> (i.e. 
> does it have a `skeletonize` function)?
>  
> -Tony
>
>
>>> El domingo, 16 de diciembre de 2012 09:41:35 UTC-5, Tony S Yu escribi?:
>>>>
>>>> On Sat, Dec 15, 2012 at 6:45 PM, Dan <dk... at walla.co.il> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Thanks for the rapid respnse, I am using 0.7.2 on windows.
>>>>>
>>>>> The error is now:
>>>>>
>>>>>  Traceback (most recent call last):
>>>>>   File "C:/Users/DK/PProjects/**skimage_seg/scikit_seg.py", line 3, 
>>>>> in <module>
>>>>>     import skimage.morphology as morph
>>>>>   File "C:\Python27\lib\site-**packages\skimage\morphology\__**init__.py", 
>>>>> line 7, in <module>
>>>>>     from ._skeletonize import skeletonize, medial_axis
>>>>> ImportError: cannot import name skeletonize
>>>>>
>>>>> Any idea why?.
>>>>>
>>>>> Thanks
>>>>>
>>>>
>>>>
>>>> Hi Dan,
>>>>
>>>> How did you install scikit-image? Also, what's the output of the 
>>>> following?
>>>>
>>>>
>>>> import skimage
>>>> print skimage.__version__
>>>> print skimage.__file__
>>>>
>>>>
>>>> -Tony
>>>>
>>>>
>>>>
>>>>> El s?bado, 15 de diciembre de 2012 16:24:31 UTC-5, Tony S Yu escribi?:
>>>>>
>>>>>> On Sat, Dec 15, 2012 at 1:58 PM, Dan <dk... at walla.co.il> wrote:
>>>>>>
>>>>>>> Dear Tony,
>>>>>>>
>>>>>>> Thanks for the script.
>>>>>>>
>>>>>>> I was running the script and I got this error:
>>>>>>> Traceback (most recent call last):
>>>>>>>   File "C:/Users/DK/PProjects/**skimage**_seg/scikit_seg.py", line 
>>>>>>> 18, in <module>
>>>>>>>     img_background = morph.reconstruction(img-h, img)
>>>>>>> AttributeError: 'module' object has no attribute 'reconstruction'
>>>>>>>
>>>>>>> Process finished with exit code 1
>>>>>>>
>>>>>>> Any reason why?
>>>>>>>
>>>>>>> Thanks a lot,
>>>>>>> Dan
>>>>>>>
>>>>>>
>>>>>> Hi Dan,
>>>>>>
>>>>>> Which version of scikit-image are you running? You'll need at least 
>>>>>> 0.7 (the latest stable release). You can check the version with the 
>>>>>> following shell command:
>>>>>>
>>>>>>     $ python -c "import skimage; print skimage.__version__"
>>>>>>
>>>>>> -Tony 
>>>>>>
>>>>>  -- 
>>  
>>  
>>
> Dear Tony,
>
> The files were a match. I uninstalled python and the other libraries, 
> installed them again and it works fine now. I do not what was the problem. 
>
> Thanks a lot for the help.
>
> Dan 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121220/0b104880/attachment.html>

From marianne.corvellec at ens-lyon.org  Thu Dec 20 04:08:41 2012
From: marianne.corvellec at ens-lyon.org (Marianne Corvellec)
Date: Thu, 20 Dec 2012 01:08:41 -0800 (PST)
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <CA+JHcKS+9R3oOssOFva4L7Y_7eaEBVeFs=4nZYq0Cgnr_2CwXQ@mail.gmail.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com>
 <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com> <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>
 <CABDkGQ=Pd0T2qLdiLoPVv2JaLcAVrxWSVLW1umQB5GK+VUbe7Q@mail.gmail.com> <02582B6B-4C51-4153-894D-7E7B64DAB5ED@gmail.com>
 <CA+JHcKS+9R3oOssOFva4L7Y_7eaEBVeFs=4nZYq0Cgnr_2CwXQ@mail.gmail.com>
Message-ID: <656792f1-e661-41ca-8ca3-bc976873d83a@googlegroups.com>

On December 14, Tony S Yu wrote:

> It might be a good idea for us to point to the stable version instead of 
> the development version by default.


+1 
For both "Gallery" and "Documentation".

On Monday, December 17, 2012 12:57:12 AM UTC+1, Juan Nunez-Iglesias wrote:
>
> Perhaps you can add a "coming soon" link to the dev gallery?
>

+1
Would act as a teaser. :)
"Coming soon" link on the "Gallery" page of stable version pointing to 
"Gallery" page of dev version.

On December 14, Stefan van der Walt wrote:

> The development gallery is useful as an advertisement, but we could 

maybe make the link to the other versions clearer?


+1
I think the above could resolve the issue.
The "Versions" box on the right-hand side is visible and great, but again, 
imho it makes more sense to point to the stable version by default.

Marianne
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121220/b2b362fb/attachment.html>

From marianne.corvellec at ens-lyon.org  Thu Dec 20 11:10:36 2012
From: marianne.corvellec at ens-lyon.org (Marianne Corvellec)
Date: Thu, 20 Dec 2012 08:10:36 -0800 (PST)
Subject: Stable vs Dev version, document image enhancement
In-Reply-To: <656792f1-e661-41ca-8ca3-bc976873d83a@googlegroups.com>
References: <a49bf6c8-0b8a-4f3d-8bb2-23e2cb8736a8@googlegroups.com>
 <ac186fe0-78ed-4ddf-a3d1-60717f7812a0@googlegroups.com> <CAEym_Hp=9WQJ0Fx8JbUuizBxCAR3pXWiSutPtLd7OJg-Cx-0Bw@mail.gmail.com>
 <CABDkGQ=Pd0T2qLdiLoPVv2JaLcAVrxWSVLW1umQB5GK+VUbe7Q@mail.gmail.com> <02582B6B-4C51-4153-894D-7E7B64DAB5ED@gmail.com>
 <CA+JHcKS+9R3oOssOFva4L7Y_7eaEBVeFs=4nZYq0Cgnr_2CwXQ@mail.gmail.com>
 <656792f1-e661-41ca-8ca3-bc976873d83a@googlegroups.com>
Message-ID: <11fb4853-a030-4701-9950-1e1b5fae5364@googlegroups.com>

My bad, I realize now it wouldn't be fine at all to point to the stable 
version 0.7.0 for documentation.
There are too many broken links, notably from the change in name 
scikits-image -> scikit-image.
So for now, let's keep pointing to the dev version by default.  When 
version 0.8 is released, we can ask the question again.

Marianne

On Thursday, December 20, 2012 10:08:41 AM UTC+1, Marianne Corvellec wrote:
>
> On December 14, Tony S Yu wrote:
>
>> It might be a good idea for us to point to the stable version instead of 
>> the development version by default.
>
>
> +1 
> For both "Gallery" and "Documentation".
>
> On Monday, December 17, 2012 12:57:12 AM UTC+1, Juan Nunez-Iglesias wrote:
>>
>> Perhaps you can add a "coming soon" link to the dev gallery?
>>
>
> +1
> Would act as a teaser. :)
> "Coming soon" link on the "Gallery" page of stable version pointing to 
> "Gallery" page of dev version.
>
> On December 14, Stefan van der Walt wrote:
>
>> The development gallery is useful as an advertisement, but we could 
>
> maybe make the link to the other versions clearer?
>
>
> +1
> I think the above could resolve the issue.
> The "Versions" box on the right-hand side is visible and great, but again, 
> imho it makes more sense to point to the stable version by default.
>
> Marianne
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121220/6b97042d/attachment.html>

From stefan at sun.ac.za  Sat Dec 22 15:41:22 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 22 Dec 2012 12:41:22 -0800
Subject: Fourier transform upsample/shift?
In-Reply-To: <cc2689cb-2de9-4178-9d82-e1fa325df391@googlegroups.com>
References: <cc2689cb-2de9-4178-9d82-e1fa325df391@googlegroups.com>
Message-ID: <CABDkGQmYJ4u0dJ1UOx-1DFzmUBxLwLV9AJ7+=ukSEpzTBCYeNg@mail.gmail.com>

Hi Adam

On Fri, Dec 21, 2012 at 8:01 PM, Adam Ginsburg <keflavich at gmail.com> wrote:
> https://github.com/keflavich/image_registration/blob/master/image_registration/fft_tools/shift.py
> https://github.com/keflavich/image_registration/blob/master/image_registration/fft_tools/scale.py
> https://github.com/keflavich/image_registration/blob/master/image_registration/fft_tools/zoom.py
> (docs here:
> https://image-registration.readthedocs.org/en/latest/fourier_tools.html)

These look interesting; do they provide any real speed-up over the
existing routines?  If so, how about using a `fourier_` prefix and
implement them all in the same file?

Regards
St?fan


From keflavich at gmail.com  Sat Dec 22 20:24:47 2012
From: keflavich at gmail.com (Adam Ginsburg)
Date: Sat, 22 Dec 2012 17:24:47 -0800 (PST)
Subject: Fourier transform upsample/shift?
In-Reply-To: <CABDkGQmYJ4u0dJ1UOx-1DFzmUBxLwLV9AJ7+=ukSEpzTBCYeNg@mail.gmail.com>
References: <cc2689cb-2de9-4178-9d82-e1fa325df391@googlegroups.com>
 <CABDkGQmYJ4u0dJ1UOx-1DFzmUBxLwLV9AJ7+=ukSEpzTBCYeNg@mail.gmail.com>
Message-ID: <f4bd778e-6969-4118-82d1-5f6236adcdf7@googlegroups.com>

Reasonable idea.  I think they are faster for at least some cases, but they 
also behave a little differently than other interpolation techniques.  So 
put them all in a "fourier_interpolation.py" file, then put them somewhere 
in transforms?

On Saturday, December 22, 2012 1:41:22 PM UTC-7, Stefan van der Walt wrote:
>
> Hi Adam 
>
> On Fri, Dec 21, 2012 at 8:01 PM, Adam Ginsburg <kefl... at gmail.com<javascript:>> 
> wrote: 
> > 
> https://github.com/keflavich/image_registration/blob/master/image_registration/fft_tools/shift.py 
> > 
> https://github.com/keflavich/image_registration/blob/master/image_registration/fft_tools/scale.py 
> > 
> https://github.com/keflavich/image_registration/blob/master/image_registration/fft_tools/zoom.py 
> > (docs here: 
> > https://image-registration.readthedocs.org/en/latest/fourier_tools.html) 
>
>
> These look interesting; do they provide any real speed-up over the 
> existing routines?  If so, how about using a `fourier_` prefix and 
> implement them all in the same file? 
>
> Regards 
> St?fan 
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121222/ea3bc59b/attachment.html>

From stefan at sun.ac.za  Sat Dec 22 22:31:48 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sat, 22 Dec 2012 19:31:48 -0800
Subject: Fourier transform upsample/shift?
In-Reply-To: <f4bd778e-6969-4118-82d1-5f6236adcdf7@googlegroups.com>
References: <cc2689cb-2de9-4178-9d82-e1fa325df391@googlegroups.com>
 <CABDkGQmYJ4u0dJ1UOx-1DFzmUBxLwLV9AJ7+=ukSEpzTBCYeNg@mail.gmail.com> <f4bd778e-6969-4118-82d1-5f6236adcdf7@googlegroups.com>
Message-ID: <CABDkGQmLaaHoeWzLnAt2bqhHHG_i_BxtBBX+Qi-151xBK60FUA@mail.gmail.com>

On Sat, Dec 22, 2012 at 5:24 PM, Adam Ginsburg <keflavich at gmail.com> wrote:
> Reasonable idea.  I think they are faster for at least some cases, but they
> also behave a little differently than other interpolation techniques.  So
> put them all in a "fourier_interpolation.py" file, then put them somewhere
> in transforms?

Yes, I think some benchmarks would be interesting.  Otherwise, we may
want to add sinc interpolation to ndimage and see if that yields the
same results.

Thanks!
St?fan


From hannesschoenberger at gmail.com  Sat Dec 22 13:50:05 2012
From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=)
Date: Sat, 22 Dec 2012 19:50:05 +0100
Subject: problem with skimage.measure.perimeter (version 0.7.1)
In-Reply-To: <aaca772e-1e4b-4c48-83ad-29c3da26a01b@googlegroups.com>
References: <aaca772e-1e4b-4c48-83ad-29c3da26a01b@googlegroups.com>
Message-ID: <CAKn83VUm2do=PUJzn_115r=GKTU==zQ2g72n9oDt132CNGpp4Q@mail.gmail.com>

Off course, you are right. I'll quickly fix this bug! Thanks for reporting.

2012/12/18 Patrice Munger <patricemunger at gmail.com>:
> Comparing the code in regionprops.py with the reference
> http://www.cs.qub.ac.uk/~d.crookes/webpubs/papers/perimeter.doc,
> should line 450 be (1 + sqrt(2) )/ 2: (13, 23) rather than 1 + sqrt(2) / 2:
> (13, 23) ?
>
> --
>
>


From hannesschoenberger at gmail.com  Sat Dec 22 14:12:06 2012
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Sch=F6nberger_Johannes?=)
Date: Sat, 22 Dec 2012 20:12:06 +0100
Subject: problem with skimage.measure.perimeter (version 0.7.1)
In-Reply-To: <CAKn83VUm2do=PUJzn_115r=GKTU==zQ2g72n9oDt132CNGpp4Q@mail.gmail.com>
References: <aaca772e-1e4b-4c48-83ad-29c3da26a01b@googlegroups.com> <CAKn83VUm2do=PUJzn_115r=GKTU==zQ2g72n9oDt132CNGpp4Q@mail.gmail.com>
Message-ID: <E5B03F6C-E7A1-4254-A1EA-DECC88D8FB78@gmail.com>

See https://github.com/scikit-image/scikit-image/pull/402.


From keflavich at gmail.com  Sun Dec 23 02:30:45 2012
From: keflavich at gmail.com (Adam)
Date: Sun, 23 Dec 2012 00:30:45 -0700
Subject: Fourier transform upsample/shift?
In-Reply-To: <CABDkGQmLaaHoeWzLnAt2bqhHHG_i_BxtBBX+Qi-151xBK60FUA@mail.gmail.com>
References: <cc2689cb-2de9-4178-9d82-e1fa325df391@googlegroups.com>
 <CABDkGQmYJ4u0dJ1UOx-1DFzmUBxLwLV9AJ7+=ukSEpzTBCYeNg@mail.gmail.com>
 <f4bd778e-6969-4118-82d1-5f6236adcdf7@googlegroups.com> <CABDkGQmLaaHoeWzLnAt2bqhHHG_i_BxtBBX+Qi-151xBK60FUA@mail.gmail.com>
Message-ID: <CAEBNSwYdGdRNxWgU84KKhYAXjDXALsC_e198HqufewNOUgG67Q@mail.gmail.com>

Benchmark tests created:
https://github.com/keflavich/image_registration/blob/master/examples/benchmarks_zoom.py
https://github.com/keflavich/image_registration/blob/master/examples/benchmarks_shift.py

They ought to be more extensive, but give the general results:
-fourier-based shifting is a little faster (maybe 50%), but follows
the same power-law
-fourier-based upsampling is marginally slower, but my test results so
far are questionable because of machine variability

Of course, with fftw3, one can increase the number of processes used
for the fft, which may speed things up.

On Sat, Dec 22, 2012 at 8:31 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
> On Sat, Dec 22, 2012 at 5:24 PM, Adam Ginsburg <keflavich at gmail.com> wrote:
>> Reasonable idea.  I think they are faster for at least some cases, but they
>> also behave a little differently than other interpolation techniques.  So
>> put them all in a "fourier_interpolation.py" file, then put them somewhere
>> in transforms?
>
> Yes, I think some benchmarks would be interesting.  Otherwise, we may
> want to add sinc interpolation to ndimage and see if that yields the
> same results.
>
> Thanks!
> St?fan
>
> --
>
>

-- 
Adam


From stefan at sun.ac.za  Sun Dec 23 06:23:58 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 23 Dec 2012 03:23:58 -0800
Subject: High order statistics/Gary level runlength matrices statistics
In-Reply-To: <e18e8310-75ad-4da5-81fb-9a26f45111d1@googlegroups.com>
References: <d8412b4c-2606-42a2-93d3-2155dde1792c@googlegroups.com> <e18e8310-75ad-4da5-81fb-9a26f45111d1@googlegroups.com>
Message-ID: <CABDkGQ=0FnKPkcqehQ3Dwx5OQaenb0c1GYmV-3+R-5wRBkgnJA@mail.gmail.com>

Hi Dan

On Sun, Dec 16, 2012 at 12:57 AM, Dan <dkin at walla.co.il> wrote:
> Is this interesting option going to be implmented in the future release?

How would you define run-length on a two-dimensional array?

Regards
St?fan


From stefan at sun.ac.za  Sun Dec 23 06:34:37 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 23 Dec 2012 03:34:37 -0800
Subject: canvastools subpackage for scikit-image viewer
In-Reply-To: <fbc88d95-3178-48fc-8828-69443b219750@googlegroups.com>
References: <CAEym_HqXtdb91_YJtNG4-CWS1XWk9azaa=G34WXZuMH7C+Kbrw@mail.gmail.com>
 <3d65b13b-c793-4337-a1fa-764e4210b264@googlegroups.com> <CAEym_Hr0e+sQ42r2ykXegXsChuUEYtU8rpEHdsanH0JTw4USog@mail.gmail.com>
 <fbc88d95-3178-48fc-8828-69443b219750@googlegroups.com>
Message-ID: <CABDkGQ=P35_2i_4zAfNGKeTTtEZZcObnP4cS6O3oga_QuzQPDQ@mail.gmail.com>

Tony and Steven,

On Fri, Dec 14, 2012 at 11:11 AM, Steven Silvester
<steven.silvester at gmail.com> wrote:
> Great, I'll dig into your PR this weekend.  I was thinking that each plugin could be registered as a dock window, and be switchable via a View menu.

Thanks for working on this--it turns out to be a very powerful
teaching and demonstration tool!

Cheers
St?fan


From stefan at sun.ac.za  Sun Dec 23 07:39:43 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Sun, 23 Dec 2012 04:39:43 -0800
Subject: "No definition found"
In-Reply-To: <CA+JHcKTLKU3bku2KayNZiwxz_PjQ9e+GHsAgNOGfT-zzFtmLmw@mail.gmail.com>
References: <CA+JHcKTLKU3bku2KayNZiwxz_PjQ9e+GHsAgNOGfT-zzFtmLmw@mail.gmail.com>
Message-ID: <CABDkGQkLjfWw1rh5CJb5u1i5ydVV1Pqdo28w+iHeS8rROTVeOw@mail.gmail.com>

On Thu, Nov 29, 2012 at 6:43 PM, Juan Nunez-Iglesias <jni.soma at gmail.com> wrote:
> I'm getting this message when trying to find the definition header for
> skimage.segmentation.slic:
>
> In [12]: %pdef segmentation.slic
> No definition header found for segmentation.slic
>
> In [15]: %pdef segmentation.join_segmentations
>  segmentation.join_segmentations(s1, s2)
>
> Anyone know why this is? Is this a general feature of Cython functions?

Not sure--but this also shows that IPython does not handle unicode
characters in a docstring correctly!  Would you like to file a bug
report?

St?fan


From hannesschoenberger at gmail.com  Sun Dec 23 03:07:43 2012
From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Sch=F6nberger_Johannes?=)
Date: Sun, 23 Dec 2012 09:07:43 +0100
Subject: Fourier transform upsample/shift?
In-Reply-To: <CAEBNSwYdGdRNxWgU84KKhYAXjDXALsC_e198HqufewNOUgG67Q@mail.gmail.com>
References: <cc2689cb-2de9-4178-9d82-e1fa325df391@googlegroups.com> <CABDkGQmYJ4u0dJ1UOx-1DFzmUBxLwLV9AJ7+=ukSEpzTBCYeNg@mail.gmail.com> <f4bd778e-6969-4118-82d1-5f6236adcdf7@googlegroups.com> <CABDkGQmLaaHoeWzLnAt2bqhHHG_i_BxtBBX+Qi-151xBK60FUA@mail.gmail.com> <CAEBNSwYdGdRNxWgU84KKhYAXjDXALsC_e198HqufewNOUgG67Q@mail.gmail.com>
Message-ID: <2E74811A-927C-4423-B795-D2893BC92330@gmail.com>

Hi,

I see you haven't benchmarked against the skimage.transform.* functions, those should be a lot faster compared to `ndimage.map_coordinates`.

If your implementation provides a different kind of interpolation, I suggest to integrate them into the current functions and add a new parameter `mode="fourier"`. I'm not sure if there is an equivalent for your functions in all cases (see `transform/_warps.py`). Thoughts?

Am 23.12.2012 um 08:30 schrieb Adam <keflavich at gmail.com>:

> Benchmark tests created:
> https://github.com/keflavich/image_registration/blob/master/examples/benchmarks_zoom.py
> https://github.com/keflavich/image_registration/blob/master/examples/benchmarks_shift.py
> 
> They ought to be more extensive, but give the general results:
> -fourier-based shifting is a little faster (maybe 50%), but follows
> the same power-law
> -fourier-based upsampling is marginally slower, but my test results so
> far are questionable because of machine variability
> 
> Of course, with fftw3, one can increase the number of processes used
> for the fft, which may speed things up.
> 
> On Sat, Dec 22, 2012 at 8:31 PM, St?fan van der Walt <stefan at sun.ac.za> wrote:
>> On Sat, Dec 22, 2012 at 5:24 PM, Adam Ginsburg <keflavich at gmail.com> wrote:
>>> Reasonable idea.  I think they are faster for at least some cases, but they
>>> also behave a little differently than other interpolation techniques.  So
>>> put them all in a "fourier_interpolation.py" file, then put them somewhere
>>> in transforms?
>> 
>> Yes, I think some benchmarks would be interesting.  Otherwise, we may
>> want to add sinc interpolation to ndimage and see if that yields the
>> same results.
>> 
>> Thanks!
>> St?fan
>> 
>> --
>> 
>> 
> 
> -- 
> Adam
> 
> -- 
> 
> 



From stefan at sun.ac.za  Wed Dec 26 16:08:59 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Wed, 26 Dec 2012 13:08:59 -0800
Subject: Testing
In-Reply-To: <76833066-56a9-422b-aacb-94230355b8e9@googlegroups.com>
References: <76833066-56a9-422b-aacb-94230355b8e9@googlegroups.com>
Message-ID: <CABDkGQ=BRPTJ-G6tBXxq9sEabV+3hQWewE0ABwTAjaJb096NFg@mail.gmail.com>

Hi Vikram

On Wed, Dec 26, 2012 at 11:36 AM, Vikram Kamath <vikram.kmth at gmail.com> wrote:
> The problem I'm having is - I've installed scikit-image and I've also forked
> the repo. I've created a branch and I'm tinkering with it. How do I run
> tests to ensure that the code, after my modification actually works?

First, you need to build the extension modules (type "make" in the
repository root).  Then, you can add that path to your PYTHONPATH:

export PYTHONPATH=$PYTHONPATH:/path/to/skimage

Then run "nosetests skimage" or

import skimage
skimage.test()

> Also, is there an IRC channel for scikit-image? . Googling for it doesn't
> show any relevant results and joining #scikit-image takes me to an empty
> channel.

Most of our communication takes place through the mailing list,
although you may receive general installation help in #scipy on
Freenode.

Good luck!
St?fan


From tsyu80 at gmail.com  Thu Dec 27 01:41:18 2012
From: tsyu80 at gmail.com (Tony Yu)
Date: Wed, 26 Dec 2012 22:41:18 -0800
Subject: canvastools subpackage for scikit-image viewer
In-Reply-To: <CABDkGQ=P35_2i_4zAfNGKeTTtEZZcObnP4cS6O3oga_QuzQPDQ@mail.gmail.com>
References: <CAEym_HqXtdb91_YJtNG4-CWS1XWk9azaa=G34WXZuMH7C+Kbrw@mail.gmail.com>
 <3d65b13b-c793-4337-a1fa-764e4210b264@googlegroups.com> <CAEym_Hr0e+sQ42r2ykXegXsChuUEYtU8rpEHdsanH0JTw4USog@mail.gmail.com>
 <fbc88d95-3178-48fc-8828-69443b219750@googlegroups.com> <CABDkGQ=P35_2i_4zAfNGKeTTtEZZcObnP4cS6O3oga_QuzQPDQ@mail.gmail.com>
Message-ID: <CAEym_HpchTrzutmv2fSdy6=kQ9o-=hh2hwytyj-Xy8+Njy8U_g@mail.gmail.com>

On Sun, Dec 23, 2012 at 3:34 AM, St?fan van der Walt <stefan at sun.ac.za>wrote:

> Tony and Steven,
>
> On Fri, Dec 14, 2012 at 11:11 AM, Steven Silvester
> <steven.silvester at gmail.com> wrote:
> > Great, I'll dig into your PR this weekend.  I was thinking that each
> plugin could be registered as a dock window, and be switchable via a View
> menu.
>
> Thanks for working on this--it turns out to be a very powerful
> teaching and demonstration tool!
>
> Cheers
> St?fan
>
>
I'm glad you like it.

I just added another tool: A canvas painter. It's a bit less responsive
than I'd like, but I think it's as fast as it'll get (it's limited by
matplotlib's blitting support for images). Check out the watershed demo in
the `viewer_examples/plugins` folder, which uses the paint tool to generate
markers for watershed segmentation.

Best,
-Tony
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121226/833673f4/attachment.html>

From stefan at sun.ac.za  Fri Dec 28 00:56:13 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Thu, 27 Dec 2012 21:56:13 -0800
Subject: canvastools subpackage for scikit-image viewer
In-Reply-To: <CAEym_HpchTrzutmv2fSdy6=kQ9o-=hh2hwytyj-Xy8+Njy8U_g@mail.gmail.com>
References: <CAEym_HqXtdb91_YJtNG4-CWS1XWk9azaa=G34WXZuMH7C+Kbrw@mail.gmail.com>
 <3d65b13b-c793-4337-a1fa-764e4210b264@googlegroups.com> <CAEym_Hr0e+sQ42r2ykXegXsChuUEYtU8rpEHdsanH0JTw4USog@mail.gmail.com>
 <fbc88d95-3178-48fc-8828-69443b219750@googlegroups.com> <CABDkGQ=P35_2i_4zAfNGKeTTtEZZcObnP4cS6O3oga_QuzQPDQ@mail.gmail.com>
 <CAEym_HpchTrzutmv2fSdy6=kQ9o-=hh2hwytyj-Xy8+Njy8U_g@mail.gmail.com>
Message-ID: <CABDkGQkz5vjLe1Nfru=mCSFiTXWdEET8miS8ce8T01UknY-VnQ@mail.gmail.com>

Hi Tony

On Wed, Dec 26, 2012 at 10:41 PM, Tony Yu <tsyu80 at gmail.com> wrote:
> I just added another tool: A canvas painter. It's a bit less responsive than
> I'd like, but I think it's as fast as it'll get (it's limited by
> matplotlib's blitting support for images). Check out the watershed demo in
> the `viewer_examples/plugins` folder, which uses the paint tool to generate
> markers for watershed segmentation.

Finally, a path to that FFT filter painter I've had in mind!  This is
very exciting.

By the way, it took me a while to figure out to press "enter" to run
the segmentation, so how about printing some instructions to the
terminal?

Thanks again,
St?fan


From emmanuelle.gouillart at nsup.org  Fri Dec 28 03:25:07 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Fri, 28 Dec 2012 09:25:07 +0100
Subject: skimage and opencv
In-Reply-To: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com>
References: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com>
Message-ID: <20121228082507.GA27386@phare.normalesup.org>

	Hi Fran??????ois,

	that's an excellent question, and not a troll :-). Opencv is a
very powerful library, but it focuses primarily on computer vision
(feature detection and extraction, classification, ...), as opposed to
image processing in general (with other tasks such as denoising,
segmentation, ...). 

	The other big difference is that skimage builds on numpy
ndarrays, and uses the full power of the numpy API (including of course
the basic facilities for processing arrays as images that come with
numpy), as well as some of scipy functions (you could have added
scipy.ndimage to your list -- a few functions in skimage are wrappers
around scipy.ndimage, that exist for the sake of completeneness). One
important consequence is that algorithms working for 3-d or even n-d
images can be easily implemented in 3-d/n-d in skimage, whereas opencv is
restricted to 2-D images (as far as I know). Thanks to the use of numpy
arrays, the API of skimage is also quite pleasant for a numpy user, more
than the API of opencv.

	A related difference is that skimage is written in python and
cython, whereas opencv is a C++ library. The two libraries attract a
different crowd of developers, and a Python/Cython toolkit based on numpy
arrays is easier to develop and maintain inside the Scientific Python
ecosystem. 

	I'm sure that other devs/users will have things to add to this
discussion!

	Cheers,
	Emmanuelle

On Thu, Dec 27, 2012 at 02:06:08PM -0800, Fran??????ois wrote:
>    Hi users and devs,

>    It came to my knowledge that another python library (based on C++ and C
>    codes) for image processing exists too : opencv
>    I understand that numpy intregrates some basic features and we need some
>    advanced features but I have the feeling that skimages is redoundant with
>    opencv in some ways.
>    What's the position of skimage about that? (Don't read this question as a
>    troll but like a real question).
>    I mean that similar features exist in both. Would not be possible to
>    reuse/integrate opencv or merge? what's the reason for keeping them apart?

>    My observation is there is 4 libraries to manipulate images:
>    * PIL
>    * numpy
>    * skimages
>    * opencv
>    That's a lot.

>    Cheers,


From stefan at sun.ac.za  Fri Dec 28 15:01:40 2012
From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=)
Date: Fri, 28 Dec 2012 12:01:40 -0800
Subject: skimage and opencv
In-Reply-To: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com>
References: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com>
Message-ID: <CABDkGQnN99ojh76bnExaYN9-kNd5pxgikCQ0XKK2rFBaFnyhcA@mail.gmail.com>

Hi Francois

On Thu, Dec 27, 2012 at 2:06 PM, Fran?ois <francois.boulogne at gmail.com> wrote:
> I understand that numpy intregrates some basic features and we need some
> advanced features but I have the feeling that skimages is redoundant with
> opencv in some ways.
> What's the position of skimage about that?

Thanks for your question--it's a good one.  There are several reasons
for a separate project, some of them already highlighted by
Emmanuelle.  A few years ago, we had to decide whether we wanted to
build on top of OpenCV, and the general consensus was that it is too
heavy a dependency.  We have three aims with `skimage`:

1. Provide a highly Pythonic interface to building blocks for
reproducible image processing reseach
2. Have simple, well-written and clear implementations of common
algorithms for use in education
3. Provide tools for solving industry problems efficiently

I think OpenCV does number 3 particularly well, while some projects
such as SimpleCV take on number 1.  But when it comes to education and
reproducible research, I believe `skimage` still holds a significant
advantage, in terms of the transparency and clarity of the code, as
well as the examples provided.

`skimage` plays particularly well with the scipy stack of tools, and I
find that the pipelining tools (dtype conversion, color space
handling, exposure adjustment, etc.) significantly improve my research
productivity.

Your comments and criticisms are most welcome; we are always keen to
hear good feedback!

Regards
St?fan


From francois.boulogne at gmail.com  Sat Dec 29 09:54:17 2012
From: francois.boulogne at gmail.com (=?UTF-8?Q?Fran=C3=A7ois?=)
Date: Sat, 29 Dec 2012 06:54:17 -0800 (PST)
Subject: skimage and opencv
In-Reply-To: <CABDkGQnN99ojh76bnExaYN9-kNd5pxgikCQ0XKK2rFBaFnyhcA@mail.gmail.com>
References: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com>
 <CABDkGQnN99ojh76bnExaYN9-kNd5pxgikCQ0XKK2rFBaFnyhcA@mail.gmail.com>
Message-ID: <bd86a54a-ca20-4d1d-90cb-8a667db9ca2c@googlegroups.com>

Many thanks for your responses. 

I agree with the fact that methods implemented in python are definitely 
easier to read. This a major advantage for education purpose. 

On the skimage home page, there is a 'Related project' box. Don't you think 
that it would be interesting to add these explanations on a dedicated page? 
Even the overview (see http://scikit-image.org/docs/dev/overview.html) is 
very light on the topic. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20121229/37b1b656/attachment.html>

From emmanuelle.gouillart at nsup.org  Sat Dec 29 10:36:49 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Sat, 29 Dec 2012 16:36:49 +0100
Subject: skimage and opencv
In-Reply-To: <bd86a54a-ca20-4d1d-90cb-8a667db9ca2c@googlegroups.com>
References: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com>
 <CABDkGQnN99ojh76bnExaYN9-kNd5pxgikCQ0XKK2rFBaFnyhcA@mail.gmail.com>
 <bd86a54a-ca20-4d1d-90cb-8a667db9ca2c@googlegroups.com>
Message-ID: <20121229153649.GA17203@phare.normalesup.org>

>    On the skimage home page, there is a 'Related project' box. Don't you
>    think that it would be interesting to add these explanations on a
>    dedicated page? Even the overview (see
>    http://scikit-image.org/docs/dev/overview.html) is very light on the
>    topic.

We welcome pull requests :-D


From emmanuelle.gouillart at nsup.org  Mon Dec 31 14:10:15 2012
From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart)
Date: Mon, 31 Dec 2012 20:10:15 +0100
Subject: the memory issue
In-Reply-To: <88d34a27-14d4-4302-bd6e-e52fdb8773d4@googlegroups.com>
References: <88d34a27-14d4-4302-bd6e-e52fdb8773d4@googlegroups.com>
Message-ID: <20121231191015.GD24873@phare.normalesup.org>

Hi Vicky,

the random walker algorithm has a quite complex api, because it can use
several modes (the 'mode' keyword argument) to solve the linear system of
the algorithm

- 'bf' (for brute force): an LU decomposition of the matrix is computed.
  This is very costly in memory, and only recommended for small images.

- 'cg' (for conjugate gradient). This mode needs much less memory, I
  suggest that you use it to test whether the algorithm gives good
results for your problem. However, this mode is quite slow.

- 'cg_mg': conjugate gradient with multigrid acceleration. This mode is
  much faster, but you'll need to install the module pyamg to use it. 

I use the cg_mg mode on tomography data (arrays of 500*500*20 float32
numbers, typically). 

Hope this helps,
Emmanuelle

On Mon, Dec 31, 2012 at 11:00:42AM -0800, vicky Liau wrote:
>    Hi everyone,
>    I use scikit-image to implement image segmentation for vegetation
>    classification. The target imagery is about 1GB, and I renewed my laptop
>    memory to 12GB (Window7 64 bit OS, CPU i7-2860QM) to read in imagery.??????
>    However, when I tried to implement random walker segmentation, ipython
>    shows memory errors.??????
>    Also, I shrink the imagery to 188 MB, and implement the same algorithm.
>    Ipython still shows errors as following.??????
>    RuntimeError ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ??????Traceback (most recent call
>    last)
>    C:\Dropbox\open_codes\RS_codes\<ipython-input-80-737c60591471> in
>    <module>()
>    ----> 1 labels = random_walker(newarray3, markers, beta=10, mode='bf')
>    C:\Python27\lib\site-packages\skimage\segmentation\random_walker_segmentation.py
>    c in random_walker(data, labels, beta, mode, tol, copy, multichannel,
>    return_ful
>    l_prob, depth)
>    ?????? ?????? 396 ?????? ?????? if mode == 'bf':
>    ?????? ?????? 397 ?????? ?????? ?????? ?????? X = _solve_bf(lap_sparse, B,
>    --> 398 ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? return_full_prob=return_full_prob)
>    ?????? ?????? 399 ?????? ?????? # Clean up results
>    ?????? ?????? 400 ?????? ?????? if return_full_prob:
>    C:\Python27\lib\site-packages\skimage\segmentation\random_walker_segmentation.py
>    c in _solve_bf(lap_sparse, B, return_full_prob)
>    ?????? ?????? 418 ?????? ?????? """
>    ?????? ?????? 419 ?????? ?????? lap_sparse = lap_sparse.tocsc()
>    --> 420 ?????? ?????? solver =
>    sparse.linalg.factorized(lap_sparse.astype(np.double))
>    ?????? ?????? 421 ?????? ?????? X = np.array([solver(np.array((-B[i]).todense()).ravel())\
>    ?????? ?????? 422 ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? for i in range(len(B))])
>    C:\Python27\lib\site-packages\scipy\sparse\linalg\dsolve\linsolve.pyc in
>    factori
>    zed(A)
>    ?????? ?????? 274
>    ?????? ?????? 275 ?????? ?????? ?????? ?????? # Make LU decomposition.
>    --> 276 ?????? ?????? ?????? ?????? umf.numeric( A )
>    ?????? ?????? 277
>    ?????? ?????? 278 ?????? ?????? ?????? ?????? def solve( b ):
>    C:\Python27\lib\site-packages\scipy\sparse\linalg\dsolve\umfpack\umfpack.pyc
>    in
>    numeric(self, mtx)
>    ?????? ?????? 401
>    ?????? ?????? 402 ?????? ?????? ?????? ?????? if self._symbolic is None:
>    --> 403 ?????? ?????? ?????? ?????? ?????? ?????? self.symbolic( mtx )
>    ?????? ?????? 404
>    ?????? ?????? 405 ?????? ?????? ?????? ?????? indx = self._getIndx( mtx )
>    C:\Python27\lib\site-packages\scipy\sparse\linalg\dsolve\umfpack\umfpack.pyc
>    in
>    symbolic(self, mtx)
>    ?????? ?????? 384 ?????? ?????? ?????? ?????? if status != UMFPACK_OK:
>    ?????? ?????? 385 ?????? ?????? ?????? ?????? ?????? ?????? raise RuntimeError('%s failed with %s' %
>    (self.funs.symbolic
>    ,
>    --> 386 ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ?????? ??????
>    ??????umfStatus[status]
>    ))
>    ?????? ?????? 387
>    ?????? ?????? 388 ?????? ?????? ?????? ?????? self.mtx = mtx
>    RuntimeError: <function umfpack_di_symbolic at 0x000000015E72F9E8> failed
>    with U
>    MFPACK_ERROR_out_of_memory
>    What can I do for that? Just want to test whether this algorithm works for
>    my thoughts.??????
>    Thanks!??????